PARADIGM pathway analysis of mRNASeq expression and copy number data
Uterine Corpus Endometrioid Carcinoma (Primary solid tumor)
15 July 2014  |  analyses__2014_07_15
Maintainer Information
Citation Information
doi:10.7908/C1GQ6WK9
Maintained by Dan DiCara (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): PARADIGM pathway analysis of mRNASeq expression and copy number data. Broad Institute of MIT and Harvard. doi:10.7908/C1GQ6WK9
Overview
Introduction

PAthway Representation and Analysis by Direct Inference on Graphical Models (PARADIGM) predicts the activity of a diverse set of molecular concepts such as genes, complexes, and processes. The predicted activities are called Inferred Pathway Levels (IPLs) and are derived from a probabilistic belief propagation strategy that incorporates multimodal data such as copy number and gene expression estimates with a concept's pathway context.

Summary

There were 54 significant pathways identified in this analysis.

Table 1.  Get Full Table Top 10 out of 131 pathways in order of significance.

Pathway.Name Avg.Num.Perturbations
Aurora B signaling 181
Endothelins 122
Aurora C signaling 118
Signaling events regulated by Ret tyrosine kinase 113
Angiopoietin receptor Tie2-mediated signaling 104
p75(NTR)-mediated signaling 98
FOXM1 transcription factor network 88
PDGFR-alpha signaling pathway 85
Signaling events mediated by the Hedgehog family 79
Integrins in angiogenesis 78
Results
Summary Table

The following list describes the columns found in Table 2.

  • Pathway.Name = Full pathway name of curated PARADIGM pathway

  • Significance.Ratio = (Ave.Num.Perturbations)/ (Cohort Size) where Cohort Size is 527 . Pathway is significant if Significance.Ratio > 0.05 .

  • Avg.Num.Perturbations = Average number of samples with perturbations across the pathway concepts determined by a background permutation model (>2 standard deviations away from the permuted distribution)

  • Total.Perturbations = Total number of perturbed concepts across all samples (>2 standard deviations away from the permuted distribution)

  • Num.Entities = Number of concepts that belong to the pathway

  • Min.Mean.Truth = Minimum IPL for concepts in the pathway among real samples

  • Max.Mean.Truth = Maximum IPL for concepts in the pathway among real samples

  • Min.Mean.Within = Minimum IPL for concepts in the pathway among null samples using "within permutation" (values are permuted across genes)

  • Max.Mean.Within = Maximum IPL for concepts in the pathway among null samples using "within permutation" (values are permuted across genes)

  • Min.Mean.Any = Minimum IPL for concepts in the pathway among null samples using "any permutation" (values are permuted across samples and genes)

  • Max.Mean.Any = Maximum IPL for concepts in the pathway among null samples using "any permutation" (values are permuted across samples and genes).

Table 2.  Get Full Table This summary table provides a report of cancer type specific pathway perturbations. Click on the links in the first column to display more detailed results for each pathway. A pathway is defined as significant (red number in Significance.Ratio column) if the Ave.Num.Perturbationsis > 5% of the cohort size ( 527 ).

Pathway.Name Significance.Ratio Avg.Num.Perturbations Total.Perturbations Num.Entities Min.Mean.Truth Max.Mean.Truth Min.Mean.Within Max.Mean.Within Min.Mean.Any Max.Mean.Within.1
Aurora B signaling 0.3435 181 12182 67 -0.29 0.37 1000 -1000 -0.029 -1000
Endothelins 0.2315 122 11776 96 -0.39 0.16 1000 -1000 -0.03 -1000
Aurora C signaling 0.2239 118 827 7 0 0.23 1000 -1000 -0.014 -1000
Signaling events regulated by Ret tyrosine kinase 0.2144 113 9314 82 -0.15 0.038 1000 -1000 -0.032 -1000
Angiopoietin receptor Tie2-mediated signaling 0.1973 104 9226 88 -0.3 0.11 1000 -1000 -0.047 -1000
p75(NTR)-mediated signaling 0.1860 98 12352 125 -0.17 0.075 1000 -1000 -0.041 -1000
FOXM1 transcription factor network 0.1670 88 4528 51 -0.28 0.28 1000 -1000 -0.06 -1000
PDGFR-alpha signaling pathway 0.1613 85 3765 44 -0.28 0.036 1000 -1000 -0.029 -1000
Signaling events mediated by the Hedgehog family 0.1499 79 4155 52 -0.2 0.11 1000 -1000 -0.02 -1000
Integrins in angiogenesis 0.1480 78 6578 84 -0.26 0.096 1000 -1000 -0.02 -1000
HIF-1-alpha transcription factor network 0.1461 77 5883 76 -0.25 0.045 1000 -1000 -0.027 -1000
PLK1 signaling events 0.1423 75 6379 85 -0.056 0.25 1000 -1000 -0.033 -1000
Reelin signaling pathway 0.1404 74 4190 56 -0.12 0.045 1000 -1000 -0.019 -1000
Cellular roles of Anthrax toxin 0.1290 68 2666 39 -0.092 0.053 1000 -1000 -0.016 -1000
Effects of Botulinum toxin 0.1271 67 1746 26 -0.1 0.11 1000 -1000 -0.008 -1000
S1P3 pathway 0.1233 65 2745 42 -0.39 0.031 1000 -1000 -0.02 -1000
Nongenotropic Androgen signaling 0.1157 61 3202 52 -0.23 0.14 1000 -1000 -0.019 -1000
Aurora A signaling 0.1082 57 3457 60 -0.14 0.22 1000 -1000 -0.015 -1000
IGF1 pathway 0.1044 55 3144 57 -0.078 0.035 1000 -1000 -0.02 -1000
Fc-epsilon receptor I signaling in mast cells 0.1025 54 5300 97 -0.096 0.024 1000 -1000 -0.031 -1000
Wnt signaling 0.1025 54 384 7 -0.066 0.035 1000 -1000 -0.007 -1000
TCGA08_retinoblastoma 0.0987 52 416 8 -0.04 0.13 1000 -1000 -0.005 -1000
FOXA2 and FOXA3 transcription factor networks 0.0930 49 2263 46 -0.19 0.18 1000 -1000 -0.047 -1000
TCGA08_p53 0.0930 49 343 7 -0.033 0.019 1000 -1000 -0.008 -1000
Signaling mediated by p38-alpha and p38-beta 0.0930 49 2175 44 -0.075 0.023 1000 -1000 -0.016 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0930 49 5969 120 -0.15 0.12 1000 -1000 -0.03 -1000
Ephrin B reverse signaling 0.0892 47 2296 48 -0.092 0.028 1000 -1000 -0.027 -1000
Thromboxane A2 receptor signaling 0.0873 46 4830 105 -0.13 0.048 1000 -1000 -0.027 -1000
Glypican 1 network 0.0873 46 2221 48 -0.17 0.1 1000 -1000 -0.021 -1000
LPA4-mediated signaling events 0.0835 44 531 12 -0.11 0 1000 -1000 -0.016 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.0816 43 2944 68 -0.15 0.075 1000 -1000 -0.053 -1000
S1P4 pathway 0.0816 43 1092 25 -0.065 0.038 1000 -1000 -0.013 -1000
Noncanonical Wnt signaling pathway 0.0797 42 1114 26 -0.12 0.035 1000 -1000 -0.023 -1000
Nephrin/Neph1 signaling in the kidney podocyte 0.0759 40 1392 34 -0.017 0.029 1000 -1000 -0.025 -1000
BMP receptor signaling 0.0759 40 3270 81 -0.23 0.043 1000 -1000 -0.026 -1000
Plasma membrane estrogen receptor signaling 0.0759 40 3474 86 -0.19 0.081 1000 -1000 -0.027 -1000
amb2 Integrin signaling 0.0740 39 3198 82 -0.1 0.13 1000 -1000 -0.017 -1000
S1P5 pathway 0.0740 39 673 17 -0.065 0.036 1000 -1000 -0.003 -1000
Syndecan-1-mediated signaling events 0.0702 37 1271 34 -0.048 0.16 1000 -1000 -0.02 -1000
LPA receptor mediated events 0.0702 37 3826 102 -0.13 0.13 1000 -1000 -0.049 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.0702 37 2951 78 -0.14 0.056 1000 -1000 -0.047 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0664 35 2975 85 -0.21 0.031 1000 -1000 -0.034 -1000
Osteopontin-mediated events 0.0645 34 1308 38 -0.087 0.096 1000 -1000 -0.019 -1000
Ephrin A reverse signaling 0.0645 34 241 7 -0.026 0.013 1000 -1000 -0.007 -1000
EPHB forward signaling 0.0626 33 2869 85 -0.055 0.048 1000 -1000 -0.044 -1000
Ras signaling in the CD4+ TCR pathway 0.0607 32 548 17 -0.09 0.023 1000 -1000 -0.017 -1000
S1P1 pathway 0.0588 31 1129 36 -0.15 0.022 1000 -1000 -0.03 -1000
Arf6 signaling events 0.0569 30 1880 62 -0.061 0.043 1000 -1000 -0.016 -1000
IL4-mediated signaling events 0.0569 30 2765 91 -0.3 0.092 1000 -1000 -0.098 -1000
Glucocorticoid receptor regulatory network 0.0550 29 3382 114 -0.15 0.21 1000 -1000 -0.035 -1000
Visual signal transduction: Rods 0.0550 29 1542 52 -0.057 0.11 1000 -1000 -0.015 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.0531 28 1565 54 -0.1 0.048 1000 -1000 -0.025 -1000
HIF-2-alpha transcription factor network 0.0531 28 1218 43 -0.16 0.076 1000 -1000 -0.042 -1000
EGFR-dependent Endothelin signaling events 0.0531 28 601 21 -0.083 0.047 1000 -1000 -0.027 -1000
FAS signaling pathway (CD95) 0.0493 26 1246 47 -0.048 0.038 1000 -1000 -0.027 -1000
Insulin Pathway 0.0493 26 1959 74 -0.097 0.11 1000 -1000 -0.031 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0474 25 1323 52 -0.055 0.047 1000 -1000 -0.022 -1000
Glypican 2 network 0.0474 25 102 4 0.023 0.043 1000 -1000 0.016 -1000
TCGA08_rtk_signaling 0.0474 25 654 26 -0.096 0.032 1000 -1000 -0.01 -1000
Coregulation of Androgen receptor activity 0.0455 24 1883 76 -0.09 0.12 1000 -1000 -0.018 -1000
Visual signal transduction: Cones 0.0455 24 939 38 -0.057 0.033 1000 -1000 -0.014 -1000
Syndecan-2-mediated signaling events 0.0455 24 1705 69 -0.01 0.1 1000 -1000 -0.027 -1000
Presenilin action in Notch and Wnt signaling 0.0455 24 1477 61 -0.087 0.083 1000 -1000 -0.035 -1000
TCR signaling in naïve CD8+ T cells 0.0455 24 2246 93 -0.014 0.052 1000 -1000 -0.034 -1000
Syndecan-4-mediated signaling events 0.0455 24 1659 67 -0.2 0.13 1000 -1000 -0.025 -1000
Signaling events mediated by PTP1B 0.0436 23 1791 76 -0.089 0.037 1000 -1000 -0.025 -1000
Calcium signaling in the CD4+ TCR pathway 0.0436 23 726 31 -0.088 0.042 1000 -1000 -0.026 -1000
Regulation of Androgen receptor activity 0.0436 23 1635 70 -0.039 0.19 1000 -1000 -0.022 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.0417 22 2858 125 -0.054 0.044 1000 -1000 -0.025 -1000
IL6-mediated signaling events 0.0417 22 1701 75 -0.086 0.089 1000 -1000 -0.028 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0417 22 740 33 -0.12 0.12 1000 -1000 -0.025 -1000
Canonical Wnt signaling pathway 0.0398 21 1102 51 -0.048 0.083 1000 -1000 -0.034 -1000
IL2 signaling events mediated by STAT5 0.0398 21 467 22 -0.096 0.076 1000 -1000 -0.023 -1000
BCR signaling pathway 0.0398 21 2176 99 -0.038 0.058 1000 -1000 -0.037 -1000
BARD1 signaling events 0.0380 20 1186 57 -0.045 0.13 1000 -1000 -0.039 -1000
Hedgehog signaling events mediated by Gli proteins 0.0380 20 1315 65 -0.093 0.052 1000 -1000 -0.028 -1000
mTOR signaling pathway 0.0380 20 1072 53 -0.029 0.025 1000 -1000 -0.024 -1000
EPO signaling pathway 0.0361 19 1078 55 -0.042 0.039 1000 -1000 -0.019 -1000
Class I PI3K signaling events mediated by Akt 0.0361 19 1306 68 -0.082 0.21 1000 -1000 -0.017 -1000
Regulation of p38-alpha and p38-beta 0.0361 19 1074 54 -0.13 0.053 1000 -1000 -0.036 -1000
IFN-gamma pathway 0.0342 18 1243 68 -0.18 0.073 1000 -1000 -0.03 -1000
Nectin adhesion pathway 0.0342 18 1179 63 -0.038 0.054 1000 -1000 -0.021 -1000
IL1-mediated signaling events 0.0342 18 1140 62 -0.026 0.068 1000 -1000 -0.024 -1000
Regulation of nuclear SMAD2/3 signaling 0.0323 17 2364 136 -0.086 0.14 1000 -1000 -0.027 -1000
IL12-mediated signaling events 0.0323 17 1539 87 -0.29 0.06 1000 -1000 -0.045 -1000
Retinoic acid receptors-mediated signaling 0.0323 17 1008 58 -0.017 0.05 1000 -1000 -0.02 -1000
Syndecan-3-mediated signaling events 0.0323 17 601 35 -0.06 0.097 1000 -1000 -0.012 -1000
Rapid glucocorticoid signaling 0.0323 17 351 20 -0.031 0.026 1000 -1000 -0.009 -1000
IL2 signaling events mediated by PI3K 0.0304 16 941 58 -0.033 0.12 1000 -1000 -0.026 -1000
PDGFR-beta signaling pathway 0.0304 16 1605 97 -0.021 0.049 1000 -1000 -0.034 -1000
ErbB2/ErbB3 signaling events 0.0285 15 1025 65 -0.073 0.048 1000 -1000 -0.041 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0285 15 436 28 -0.065 0.041 1000 -1000 -0.015 -1000
Insulin-mediated glucose transport 0.0285 15 499 32 -0.083 0.21 1000 -1000 -0.018 -1000
FoxO family signaling 0.0285 15 1005 64 -0.016 0.21 1000 -1000 -0.031 -1000
Regulation of Telomerase 0.0285 15 1573 102 -0.24 0.086 1000 -1000 -0.036 -1000
IL23-mediated signaling events 0.0285 15 922 60 -0.007 0.23 1000 -1000 -0.051 -1000
JNK signaling in the CD4+ TCR pathway 0.0266 14 249 17 -0.045 0.056 1000 -1000 -0.014 -1000
Ceramide signaling pathway 0.0266 14 1096 76 -0.048 0.06 1000 -1000 -0.025 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0266 14 640 45 -0.005 0.057 1000 -1000 -0.032 -1000
Signaling events mediated by PRL 0.0266 14 483 34 -0.037 0.091 1000 -1000 -0.029 -1000
Caspase cascade in apoptosis 0.0247 13 1020 74 -0.029 0.15 1000 -1000 -0.026 -1000
ceramide signaling pathway 0.0247 13 644 49 -0.01 0.054 1000 -1000 -0.027 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0247 13 1156 83 -0.022 0.21 1000 -1000 -0.019 -1000
ErbB4 signaling events 0.0228 12 833 69 -0.049 0.055 1000 -1000 -0.025 -1000
E-cadherin signaling in keratinocytes 0.0228 12 529 43 -0.008 0.038 1000 -1000 -0.016 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0209 11 411 37 -0.021 0.063 1000 -1000 -0.015 -1000
Signaling mediated by p38-gamma and p38-delta 0.0209 11 170 15 -0.011 0.022 1000 -1000 -0.017 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0209 11 852 74 -0.048 0.077 1000 -1000 -0.045 -1000
IL27-mediated signaling events 0.0190 10 555 51 -0.032 0.039 1000 -1000 -0.028 -1000
E-cadherin signaling in the nascent adherens junction 0.0190 10 799 76 -0.03 0.056 1000 -1000 -0.035 -1000
Class IB PI3K non-lipid kinase events 0.0190 10 30 3 -0.022 0.022 1000 -1000 -0.02 -1000
Canonical NF-kappaB pathway 0.0171 9 374 39 -0.008 0.053 1000 -1000 -0.017 -1000
Signaling events mediated by HDAC Class III 0.0171 9 386 40 -0.052 0.04 1000 -1000 -0.03 -1000
Signaling events mediated by HDAC Class II 0.0133 7 564 75 -0.033 0.044 1000 -1000 -0.02 -1000
Arf6 trafficking events 0.0133 7 500 71 -0.16 0.041 1000 -1000 -0.032 -1000
p38 MAPK signaling pathway 0.0133 7 343 44 -0.003 0.064 1000 -1000 -0.018 -1000
Class I PI3K signaling events 0.0114 6 446 73 -0.023 0.042 1000 -1000 -0.023 -1000
Signaling events mediated by HDAC Class I 0.0095 5 558 104 -0.035 0.057 1000 -1000 -0.035 -1000
Arf6 downstream pathway 0.0076 4 173 43 -0.037 0.041 1000 -1000 -0.024 -1000
TRAIL signaling pathway 0.0076 4 238 48 -0.01 0.049 1000 -1000 -0.019 -1000
Paxillin-dependent events mediated by a4b1 0.0076 4 170 36 -0.041 0.043 1000 -1000 -0.028 -1000
VEGFR1 specific signals 0.0076 4 259 56 -0.041 0.047 1000 -1000 -0.025 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0057 3 77 23 0.002 0.045 1000 -1000 -0.022 -1000
PLK2 and PLK4 events 0.0057 3 11 3 -0.011 0.025 1000 -1000 -0.013 -1000
Arf1 pathway 0.0057 3 180 54 -0.006 0.041 1000 -1000 -0.009 -1000
a4b1 and a4b7 Integrin signaling 0.0038 2 10 5 0.022 0.033 1000 -1000 0.018 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0038 2 56 27 -0.013 0.054 1000 -1000 -0.025 -1000
Atypical NF-kappaB pathway 0.0019 1 48 31 -0.011 0.026 1000 -1000 -0.016 -1000
E-cadherin signaling events 0.0019 1 7 5 0.019 0.038 1000 -1000 0.018 -1000
Circadian rhythm pathway 0.0000 0 16 22 -0.005 0.048 1000 -1000 -0.031 -1000
Alternative NF-kappaB pathway 0.0000 0 2 13 0 0.059 1000 -1000 0 -1000
Total NA 4152 248807 7203 -12 10 131000 -131000 -3.2 -131000
Aurora B signaling

Figure S1.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S1.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Condensin I complex 0.13 0.094 0.19 273 -0.3 6 279
STMN1 0.089 0.045 0.11 413 -10000 0 413
Aurora B/RasGAP/Survivin 0.26 0.15 0.33 412 -0.15 11 423
Chromosomal passenger complex/Cul3 protein complex 0.078 0.099 0.17 190 -0.28 5 195
BIRC5 0.23 0.11 0.29 397 -10000 0 397
DES -0.29 0.24 -10000 0 -0.56 111 111
Aurora C/Aurora B/INCENP 0.16 0.084 0.2 401 -10000 0 401
Aurora B/TACC1 0.082 0.15 0.19 313 -0.2 84 397
Aurora B/PP2A 0.17 0.079 0.21 406 -10000 0 406
mol:GTP 0 0 -10000 0 -10000 0 0
CBX5 0.042 0.026 0.12 23 -10000 0 23
mitotic metaphase/anaphase transition -0.008 0.005 -10000 0 -10000 0 0
NDC80 0.098 0.074 0.12 414 -10000 0 414
Cul3 protein complex -0.003 0.099 -10000 0 -0.21 96 96
KIF2C 0.15 0.076 0.21 301 -10000 0 301
PEBP1 0.024 0.003 -10000 0 -10000 0 0
KIF20A 0.25 0.082 0.28 461 -10000 0 461
mol:GDP 0 0 -10000 0 -10000 0 0
Aurora B/RasGAP 0.16 0.088 0.21 400 -0.23 5 405
SEPT1 0.021 0.017 -10000 0 -0.35 1 1
SMC2 0.022 0.013 0.28 1 -10000 0 1
SMC4 0.022 0.005 -10000 0 -10000 0 0
NSUN2/NPM1/Nucleolin 0.11 0.17 0.29 22 -0.42 40 62
PSMA3 0.022 0.004 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.006 0.005 -10000 0 -10000 0 0
H3F3B 0.091 0.049 0.22 18 -10000 0 18
AURKB 0.24 0.11 0.29 418 -10000 0 418
AURKC 0.023 0.016 0.28 2 -10000 0 2
CDCA8 0.18 0.13 0.29 301 -10000 0 301
cytokinesis 0.14 0.092 0.22 251 -0.3 1 252
Aurora B/Septin1 0.21 0.14 0.29 341 -0.27 7 348
AURKA 0.093 0.12 0.28 154 -10000 0 154
INCENP 0.03 0.006 -10000 0 -10000 0 0
KLHL13 -0.049 0.15 -10000 0 -0.35 100 100
BUB1 0.21 0.12 0.28 402 -10000 0 402
hSgo1/Aurora B/Survivin 0.36 0.19 0.44 434 -0.16 2 436
EVI5 0.03 0.005 -10000 0 -10000 0 0
RhoA/GTP 0.16 0.088 0.23 196 -0.26 2 198
SGOL1 0.22 0.11 0.28 392 -10000 0 392
CENPA 0.18 0.11 0.24 363 -0.28 5 368
NCAPG 0.19 0.12 0.28 335 -10000 0 335
Aurora B/HC8 Proteasome 0.17 0.077 0.21 411 -10000 0 411
NCAPD2 0.022 0.004 -10000 0 -10000 0 0
Aurora B/PP1-gamma 0.17 0.076 0.21 414 -10000 0 414
RHOA 0.022 0.005 -10000 0 -10000 0 0
NCAPH 0.22 0.11 0.28 402 -10000 0 402
NPM1 0.087 0.12 0.25 4 -0.33 32 36
RASA1 0.019 0.037 -10000 0 -0.35 5 5
KLHL9 0.021 0.017 -10000 0 -0.35 1 1
mitotic prometaphase 0 0.001 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.17 0.077 0.21 411 -10000 0 411
PPP1CC 0.023 0.002 -10000 0 -10000 0 0
Centraspindlin 0.18 0.096 0.24 294 -0.28 2 296
RhoA/GDP 0.016 0.004 -10000 0 -10000 0 0
NSUN2 0.099 0.1 0.26 18 -0.28 26 44
MYLK -0.079 0.16 0.22 6 -0.22 287 293
KIF23 0.04 0.052 0.29 21 -10000 0 21
VIM 0.092 0.072 0.12 409 -0.23 6 415
RACGAP1 0.031 0.018 0.3 2 -10000 0 2
mitosis 0 0 -10000 0 -10000 0 0
NCL 0.09 0.12 0.23 1 -0.34 29 30
Chromosomal passenger complex 0.19 0.094 0.23 393 -0.29 3 396
Chromosomal passenger complex/EVI5 0.37 0.19 0.45 411 -10000 0 411
TACC1 -0.04 0.14 -10000 0 -0.35 84 84
PPP2R5D 0.023 0.004 -10000 0 -10000 0 0
CUL3 0.023 0.003 -10000 0 -10000 0 0
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
Endothelins

Figure S2.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S2.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
AKT1 -0.14 0.15 -10000 0 -0.3 193 193
PTK2B 0.02 0.008 -10000 0 -10000 0 0
mol:Ca2+ -0.2 0.31 -10000 0 -0.75 104 104
EDN1 -0.054 0.08 -10000 0 -0.24 44 44
EDN3 0.029 0.16 0.28 93 -0.35 54 147
EDN2 0.064 0.095 0.28 82 -10000 0 82
HRAS/GDP -0.19 0.22 -10000 0 -0.47 147 147
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.13 0.18 -10000 0 -0.37 136 136
ADCY4 -0.14 0.16 0.3 1 -0.32 170 171
ADCY5 -0.16 0.16 0.24 2 -0.33 203 205
ADCY6 -0.14 0.15 0.22 3 -0.31 176 179
ADCY7 -0.13 0.15 0.24 2 -0.32 162 164
ADCY1 -0.14 0.16 0.24 2 -0.32 171 173
ADCY2 -0.21 0.18 0.18 1 -0.36 269 270
ADCY3 -0.13 0.15 0.24 2 -0.32 161 163
ADCY8 -0.13 0.15 -10000 0 -0.31 163 163
ADCY9 -0.15 0.18 0.3 1 -0.35 179 180
arachidonic acid secretion -0.23 0.27 -10000 0 -0.5 216 216
ETB receptor/Endothelin-1/Gq/GTP -0.085 0.15 -10000 0 -0.28 151 151
GNAO1 -0.065 0.16 -10000 0 -0.35 120 120
HRAS 0.021 0.005 -10000 0 -10000 0 0
ETA receptor/Endothelin-1/G12/GTP -0.12 0.14 -10000 0 -0.28 188 188
ETA receptor/Endothelin-1/Gs/GTP -0.14 0.16 -10000 0 -0.3 198 198
mol:GTP -0.003 0.005 -10000 0 -10000 0 0
COL3A1 -0.15 0.17 -10000 0 -0.34 174 174
EDNRB -0.057 0.15 -10000 0 -0.35 109 109
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.17 0.2 -10000 0 -0.42 157 157
CYSLTR1 -0.14 0.16 -10000 0 -0.35 146 146
SLC9A1 -0.086 0.097 -10000 0 -0.2 180 180
mol:GDP -0.2 0.24 -10000 0 -0.49 156 156
SLC9A3 -0.2 0.32 -10000 0 -0.69 134 134
RAF1 -0.22 0.25 -10000 0 -0.48 200 200
JUN -0.18 0.28 -10000 0 -0.69 100 100
JAK2 -0.14 0.15 -10000 0 -0.31 188 188
mol:IP3 -0.14 0.19 -10000 0 -0.43 115 115
ETA receptor/Endothelin-1 -0.16 0.18 -10000 0 -0.35 200 200
PLCB1 0.013 0.031 -10000 0 -0.35 3 3
PLCB2 0.011 0.019 -10000 0 -10000 0 0
ETA receptor/Endothelin-3 -0.096 0.18 0.21 31 -0.3 184 215
FOS -0.33 0.39 -10000 0 -0.82 185 185
Gai/GDP -0.26 0.39 -10000 0 -0.77 176 176
CRK 0.021 0.006 -10000 0 -10000 0 0
mol:Ca ++ -0.19 0.22 -10000 0 -0.43 187 187
BCAR1 0.021 0.008 -10000 0 -10000 0 0
PRKCB1 -0.13 0.19 -10000 0 -0.42 116 116
GNAQ 0.008 0.026 -10000 0 -0.35 1 1
GNAZ 0.011 0.062 -10000 0 -0.35 15 15
GNAL -0.031 0.13 -10000 0 -0.35 74 74
Gs family/GDP -0.2 0.22 -10000 0 -0.46 167 167
ETA receptor/Endothelin-1/Gq/GTP -0.14 0.19 -10000 0 -0.36 165 165
MAPK14 -0.084 0.14 0.2 2 -0.34 90 92
TRPC6 -0.21 0.34 -10000 0 -0.8 104 104
GNAI2 0.022 0.005 -10000 0 -10000 0 0
GNAI3 0.023 0.002 -10000 0 -10000 0 0
GNAI1 0.017 0.046 -10000 0 -0.35 8 8
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.086 0.15 -10000 0 -0.34 98 98
ETB receptor/Endothelin-2 -0.006 0.13 0.21 55 -0.24 105 160
ETB receptor/Endothelin-3 -0.022 0.17 0.21 83 -0.28 134 217
ETB receptor/Endothelin-1 -0.079 0.12 -10000 0 -0.28 121 121
MAPK3 -0.32 0.37 -10000 0 -0.77 189 189
MAPK1 -0.32 0.37 -10000 0 -0.77 190 190
Rac1/GDP -0.19 0.22 -10000 0 -0.47 147 147
cAMP biosynthetic process -0.21 0.21 0.3 4 -0.42 205 209
MAPK8 -0.22 0.35 -10000 0 -0.8 108 108
SRC 0.022 0.005 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP -0.1 0.15 -10000 0 -0.27 199 199
p130Cas/CRK/Src/PYK2 -0.2 0.26 0.25 1 -0.57 131 132
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.18 0.22 -10000 0 -0.47 145 145
COL1A2 -0.17 0.2 -10000 0 -0.43 145 145
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 -0.082 0.16 0.2 41 -0.28 162 203
mol:DAG -0.14 0.19 -10000 0 -0.43 115 115
MAP2K2 -0.26 0.29 -10000 0 -0.59 202 202
MAP2K1 -0.26 0.29 -10000 0 -0.59 200 200
EDNRA -0.15 0.18 -10000 0 -0.38 177 177
positive regulation of muscle contraction -0.12 0.13 0.2 2 -0.27 169 171
Gq family/GDP -0.16 0.22 -10000 0 -0.46 137 137
HRAS/GTP -0.19 0.23 -10000 0 -0.48 148 148
PRKCH -0.14 0.19 0.21 2 -0.42 116 118
RAC1 0.022 0.005 -10000 0 -10000 0 0
PRKCA -0.14 0.19 0.21 1 -0.42 116 117
PRKCB -0.14 0.19 -10000 0 -0.43 121 121
PRKCE -0.13 0.18 -10000 0 -0.42 113 113
PRKCD -0.13 0.19 0.21 1 -0.42 112 113
PRKCG -0.14 0.19 -10000 0 -0.42 115 115
regulation of vascular smooth muscle contraction -0.39 0.46 -10000 0 -0.98 185 185
PRKCQ -0.14 0.2 0.2 1 -0.41 134 135
PLA2G4A -0.26 0.3 -10000 0 -0.56 216 216
GNA14 -0.022 0.1 -10000 0 -0.35 44 44
GNA15 0.018 0.033 0.27 7 -10000 0 7
GNA12 0.022 0.005 -10000 0 -10000 0 0
GNA11 0.008 0.05 -10000 0 -0.35 9 9
Rac1/GTP -0.12 0.14 -10000 0 -0.28 192 192
MMP1 0.16 0.14 0.35 117 -10000 0 117
Aurora C signaling

Figure S3.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S3.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
INCENP 0.023 0.003 -10000 0 -10000 0 0
Aurora C/Aurora B/INCENP 0.15 0.083 0.19 401 -10000 0 401
metaphase 0 0 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
H3F3B 0.011 0.039 -10000 0 -0.34 6 6
AURKB 0.23 0.1 0.28 418 -10000 0 418
AURKC 0.023 0.016 0.28 2 -10000 0 2
Signaling events regulated by Ret tyrosine kinase

Figure S4.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S4.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 -0.02 0.061 -10000 0 -0.39 9 9
Crk/p130 Cas/Paxillin -0.12 0.13 -10000 0 -0.26 203 203
JUN -0.086 0.12 0.14 1 -0.21 217 218
HRAS 0.022 0.005 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/GRB10 -0.062 0.14 0.23 13 -0.2 233 246
RAP1A 0.023 0.001 -10000 0 -10000 0 0
FRS2 0.023 0.003 -10000 0 -10000 0 0
RAP1A/GDP 0.017 0.001 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 -0.061 0.14 0.23 14 -0.2 231 245
EntrezGene:5979 0 0 -10000 0 -10000 0 0
PTPN11 0.023 0.003 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.021 0.006 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma -0.061 0.11 0.27 2 -0.19 225 227
RHOA 0.022 0.005 -10000 0 -10000 0 0
RAP1A/GTP -0.057 0.12 0.43 1 -0.18 233 234
GRB7 0.038 0.074 0.32 30 -0.35 2 32
RET51/GFRalpha1/GDNF -0.06 0.14 0.23 13 -0.2 227 240
MAPKKK cascade -0.08 0.12 0.32 1 -0.22 216 217
BCAR1 0.02 0.007 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/IRS1 -0.078 0.13 0.27 2 -0.21 244 246
lamellipodium assembly -0.11 0.13 -10000 0 -0.24 212 212
RET51/GFRalpha1/GDNF/SHC -0.049 0.13 0.25 6 -0.21 187 193
PIK3CA 0.02 0.018 -10000 0 -0.35 1 1
RET9/GFRalpha1/GDNF/SHC -0.047 0.1 0.31 1 -0.19 179 180
RET9/GFRalpha1/GDNF/Shank3 -0.063 0.11 0.27 2 -0.19 227 229
MAPK3 -0.076 0.11 0.24 21 -0.31 20 41
DOK1 0.023 0.003 -10000 0 -10000 0 0
DOK6 -0.046 0.14 -10000 0 -0.35 95 95
PXN 0.023 0.003 -10000 0 -10000 0 0
neurite development -0.089 0.12 0.28 12 -0.26 80 92
DOK5 -0.011 0.11 0.28 1 -0.35 46 47
GFRA1 -0.15 0.19 0.28 2 -0.35 235 237
MAPK8 -0.087 0.12 0.16 2 -0.21 219 221
HRAS/GTP -0.077 0.15 0.44 1 -0.23 224 225
tube development -0.057 0.11 0.21 8 -0.18 222 230
MAPK1 -0.076 0.11 0.25 20 -0.31 20 40
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.076 0.1 0.15 1 -0.19 223 224
Rac1/GDP 0.016 0.003 -10000 0 -10000 0 0
SRC 0.022 0.005 -10000 0 -10000 0 0
PDLIM7 0.022 0.005 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok6 -0.082 0.16 0.5 1 -0.23 255 256
SHC1 0.019 0.009 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 -0.064 0.14 0.25 7 -0.2 233 240
RET51/GFRalpha1/GDNF/Dok5 -0.076 0.15 0.23 12 -0.23 239 251
PRKCA 0 0.087 -10000 0 -0.35 30 30
HRAS/GDP 0.016 0.004 -10000 0 -10000 0 0
CREB1 -0.076 0.13 0.21 2 -0.24 177 179
PIK3R1 0.018 0.037 -10000 0 -0.35 5 5
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.063 0.1 0.19 2 -0.2 179 181
RET51/GFRalpha1/GDNF/Grb7 -0.054 0.15 0.24 29 -0.21 227 256
mol:GDP 0 0 -10000 0 -10000 0 0
RET 0.013 0.099 0.28 21 -0.35 27 48
DOK4 0.021 0.007 -10000 0 -10000 0 0
JNK cascade -0.085 0.12 -10000 0 -0.35 35 35
RET9/GFRalpha1/GDNF/FRS2 -0.062 0.11 0.27 2 -0.19 227 229
SHANK3 0.021 0.007 -10000 0 -10000 0 0
RASA1 0.019 0.037 -10000 0 -0.35 5 5
NCK1 0.021 0.023 -10000 0 -0.35 2 2
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.06 0.098 0.19 2 -0.19 176 178
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.081 0.12 0.22 1 -0.21 229 230
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.083 0.13 0.19 2 -0.22 222 224
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.067 0.12 0.18 8 -0.22 181 189
PI3K -0.15 0.19 0.3 1 -0.35 210 211
SOS1 0.023 0.003 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.053 0.11 0.26 2 -0.18 222 224
GRB10 0.022 0.017 -10000 0 -0.35 1 1
activation of MAPKK activity -0.072 0.11 0.18 1 -0.2 216 217
RET51/GFRalpha1/GDNF/FRS2 -0.061 0.14 0.23 14 -0.2 232 246
GAB1 0.019 0.033 -10000 0 -0.35 4 4
IRS1 -0.013 0.11 -10000 0 -0.35 50 50
IRS2 -0.026 0.12 -10000 0 -0.35 67 67
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.07 0.13 0.18 8 -0.22 182 190
RET51/GFRalpha1/GDNF/PKC alpha -0.073 0.15 0.25 8 -0.22 242 250
GRB2 0.022 0.006 -10000 0 -10000 0 0
PRKACA 0.022 0.005 -10000 0 -10000 0 0
GDNF 0.02 0.02 0.28 3 -10000 0 3
RAC1 0.022 0.005 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 -0.077 0.15 0.23 13 -0.22 247 260
Rac1/GTP -0.12 0.16 0.25 1 -0.29 208 209
RET9/GFRalpha1/GDNF -0.075 0.12 0.27 2 -0.2 228 230
GFRalpha1/GDNF -0.092 0.14 0.3 2 -0.25 228 230
Angiopoietin receptor Tie2-mediated signaling

Figure S5.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S5.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
AKT1 -0.22 0.41 0.46 2 -0.81 163 165
NCK1/PAK1/Dok-R -0.13 0.18 -10000 0 -0.4 161 161
NCK1/Dok-R -0.26 0.48 -10000 0 -0.94 159 159
PIK3CA 0.02 0.018 -10000 0 -0.35 1 1
mol:beta2-estradiol 0.046 0.092 0.23 105 -10000 0 105
RELA 0.022 0.004 -10000 0 -10000 0 0
SHC1 0.018 0.009 -10000 0 -10000 0 0
Rac/GDP 0.016 0.003 -10000 0 -10000 0 0
F2 0.077 0.12 0.28 139 -10000 0 139
TNIP2 0.022 0.005 -10000 0 -10000 0 0
NF kappa B/RelA -0.24 0.45 -10000 0 -0.88 161 161
FN1 0.019 0.036 -10000 0 -0.35 5 5
PLD2 -0.28 0.49 -10000 0 -0.98 158 158
PTPN11 0.023 0.003 -10000 0 -10000 0 0
GRB14 0.11 0.13 0.28 186 -0.35 2 188
ELK1 -0.26 0.44 -10000 0 -0.89 161 161
GRB7 0.038 0.074 0.32 30 -0.35 2 32
PAK1 0.022 0.004 -10000 0 -10000 0 0
Tie2/Ang1/alpha5/beta1 Integrin -0.25 0.48 -10000 0 -0.93 160 160
CDKN1A -0.14 0.29 0.47 1 -0.56 152 153
ITGA5 0.023 0.003 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.26 0.48 -10000 0 -0.94 160 160
CRK 0.021 0.006 -10000 0 -10000 0 0
mol:NO -0.16 0.31 0.4 3 -0.6 163 166
PLG -0.3 0.49 -10000 0 -0.99 158 158
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis -0.22 0.38 -10000 0 -0.77 163 163
GRB2 0.022 0.006 -10000 0 -10000 0 0
PIK3R1 0.018 0.037 -10000 0 -0.35 5 5
ANGPT2 -0.1 0.22 -10000 0 -0.59 52 52
BMX -0.3 0.5 -10000 0 -1 160 160
ANGPT1 -0.22 0.44 -10000 0 -1.1 105 105
tube development -0.17 0.32 0.58 1 -0.61 162 163
ANGPT4 0.006 0.04 0.28 2 -0.35 4 6
response to hypoxia -0.019 0.03 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.24 0.54 -10000 0 -1 160 160
alpha5/beta1 Integrin 0.033 0.007 -10000 0 -10000 0 0
FGF2 -0.17 0.18 -10000 0 -0.35 265 265
STAT5A (dimer) -0.18 0.36 0.43 1 -0.69 160 161
mol:L-citrulline -0.16 0.31 0.4 3 -0.6 163 166
AGTR1 -0.054 0.15 0.29 2 -0.35 106 108
MAPK14 -0.29 0.51 -10000 0 -1 163 163
Tie2/SHP2 -0.19 0.4 -10000 0 -0.99 96 96
TEK -0.21 0.44 -10000 0 -1.1 94 94
RPS6KB1 -0.21 0.4 0.39 1 -0.78 163 164
Angiotensin II/AT1 -0.035 0.1 0.21 2 -0.24 106 108
Tie2/Ang1/GRB2 -0.28 0.51 -10000 0 -1 161 161
MAPK3 -0.26 0.45 -10000 0 -0.91 157 157
MAPK1 -0.26 0.45 -10000 0 -0.91 158 158
Tie2/Ang1/GRB7 -0.28 0.51 -10000 0 -0.99 161 161
NFKB1 0.022 0.017 -10000 0 -0.35 1 1
MAPK8 -0.29 0.49 -10000 0 -0.98 160 160
PI3K -0.26 0.47 -10000 0 -0.93 163 163
FES -0.29 0.51 -10000 0 -1 163 163
Crk/Dok-R -0.26 0.48 -10000 0 -0.94 160 160
Tie2/Ang1/ABIN2 -0.28 0.51 -10000 0 -1 161 161
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity -0.19 0.37 0.45 2 -0.72 163 165
STAT5A 0.021 0.017 -10000 0 -0.35 1 1
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 -0.2 0.4 0.52 2 -0.78 161 163
Tie2/Ang2 -0.23 0.42 0.44 1 -0.82 158 159
Tie2/Ang1 -0.3 0.54 -10000 0 -1.1 160 160
FOXO1 -0.19 0.37 0.46 2 -0.73 163 165
ELF1 -0.006 0.059 -10000 0 -0.13 67 67
ELF2 -0.28 0.49 -10000 0 -0.98 158 158
mol:Choline -0.27 0.46 -10000 0 -0.94 158 158
cell migration -0.07 0.1 -10000 0 -0.22 162 162
FYN -0.19 0.36 0.59 1 -0.69 162 163
DOK2 0.022 0.021 0.28 3 -10000 0 3
negative regulation of cell cycle -0.13 0.26 0.46 1 -0.5 159 160
ETS1 -0.032 0.11 -10000 0 -0.24 100 100
PXN -0.16 0.34 0.43 5 -0.65 160 165
ITGB1 0.022 0.004 -10000 0 -10000 0 0
NOS3 -0.18 0.35 0.41 3 -0.69 163 166
RAC1 0.022 0.005 -10000 0 -10000 0 0
TNF -0.006 0.14 0.28 54 -0.24 104 158
MAPKKK cascade -0.27 0.46 -10000 0 -0.94 158 158
RASA1 0.019 0.037 -10000 0 -0.35 5 5
Tie2/Ang1/Shc -0.28 0.5 -10000 0 -0.98 161 161
NCK1 0.021 0.023 -10000 0 -0.35 2 2
vasculogenesis -0.14 0.28 0.4 3 -0.54 163 166
mol:Phosphatidic acid -0.27 0.46 -10000 0 -0.94 158 158
mol:Angiotensin II 0.001 0.001 -10000 0 -10000 0 0
mol:NADP -0.16 0.31 0.4 3 -0.6 163 166
Rac1/GTP -0.2 0.37 -10000 0 -0.73 163 163
MMP2 -0.29 0.49 -10000 0 -1 158 158
p75(NTR)-mediated signaling

Figure S6.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S6.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Sortilin/TRAF6 0.032 0.008 -10000 0 -10000 0 0
Necdin/E2F1 -0.076 0.15 0.21 36 -0.24 227 263
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E -0.057 0.15 -10000 0 -0.22 214 214
NGF (dimer)/p75(NTR)/BEX1 -0.12 0.18 0.2 3 -0.29 261 264
NT-4/5 (dimer)/p75(NTR) -0.051 0.14 0.22 18 -0.25 165 183
IKBKB 0.021 0.007 -10000 0 -10000 0 0
AKT1 -0.084 0.12 0.17 31 -0.22 192 223
IKBKG 0.023 0.003 -10000 0 -10000 0 0
BDNF 0.061 0.093 0.28 79 -10000 0 79
MGDIs/NGR/p75(NTR)/LINGO1 -0.036 0.12 0.2 6 -0.21 165 171
FURIN 0.022 0.004 -10000 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin -0.017 0.14 0.2 67 -0.21 165 232
LINGO1 0.024 0.03 0.28 5 -0.35 1 6
Sortilin/TRAF6/NRIF 0.018 0.026 -10000 0 -0.17 6 6
proBDNF (dimer) 0.061 0.092 0.28 79 -10000 0 79
NTRK1 0.019 0.045 0.28 7 -0.35 4 11
RTN4R 0.021 0.017 -10000 0 -0.35 1 1
neuron apoptosis -0.077 0.15 -10000 0 -0.36 60 60
IRAK1 0.023 0.004 -10000 0 -10000 0 0
SHC1 -0.095 0.12 -10000 0 -0.25 184 184
ARHGDIA 0.022 0.005 -10000 0 -10000 0 0
RhoA/GTP 0.016 0.004 -10000 0 -10000 0 0
Gamma Secretase 0.045 0.04 -10000 0 -0.18 6 6
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 -0.11 0.18 0.21 1 -0.27 267 268
MAGEH1 -0.069 0.16 -10000 0 -0.35 128 128
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.16 0.18 -10000 0 -0.28 330 330
Mammalian IAPs/DIABLO 0.053 0.033 -10000 0 -0.19 7 7
proNGF (dimer) -0.057 0.15 -10000 0 -0.35 112 112
MAGED1 0.021 0.023 -10000 0 -0.35 2 2
APP 0.023 0.004 -10000 0 -10000 0 0
NT-4/5 (dimer) 0.031 0.055 0.28 22 -0.35 1 23
ZNF274 0.022 0.005 -10000 0 -10000 0 0
RhoA/GDP/RHOGDI -0.073 0.13 -10000 0 -0.22 211 211
NGF -0.057 0.15 -10000 0 -0.35 112 112
cell cycle arrest -0.079 0.11 0.18 3 -0.2 176 179
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK -0.084 0.14 -10000 0 -0.25 198 198
NT-4/5 (dimer)/p75(NTR)/TRAF6 -0.033 0.12 0.21 16 -0.21 164 180
NCSTN 0.019 0.009 -10000 0 -10000 0 0
mol:GTP -0.083 0.16 0.2 1 -0.25 220 221
PSENEN 0.022 0.005 -10000 0 -10000 0 0
mol:ceramide -0.1 0.12 0.18 3 -0.23 209 212
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs -0.074 0.12 -10000 0 -0.33 65 65
p75(NTR)/beta APP -0.056 0.13 0.21 1 -0.24 165 166
BEX1 -0.051 0.15 0.28 2 -0.35 104 106
mol:GDP -0.11 0.13 -10000 0 -0.25 217 217
NGF (dimer) -0.016 0.14 0.21 39 -0.21 156 195
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI -0.024 0.12 0.21 6 -0.19 164 170
PIK3R1 0.018 0.037 -10000 0 -0.35 5 5
RAC1/GTP -0.067 0.13 0.18 1 -0.21 214 215
MYD88 0.022 0.004 -10000 0 -10000 0 0
CHUK 0.022 0.005 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA -0.083 0.16 0.2 1 -0.25 220 221
RHOB 0.022 0.017 -10000 0 -0.35 1 1
RHOA 0.022 0.005 -10000 0 -10000 0 0
MAGE-G1/E2F1 0.062 0.069 0.21 89 -10000 0 89
NT3 (dimer) 0.003 0.091 0.28 5 -0.35 30 35
TP53 -0.054 0.087 0.18 7 -10000 0 7
PRDM4 -0.1 0.12 0.18 3 -0.23 212 215
BDNF (dimer) 0.075 0.14 0.24 160 -0.19 70 230
PIK3CA 0.02 0.018 -10000 0 -0.35 1 1
SORT1 0.023 0.003 -10000 0 -10000 0 0
activation of caspase activity -0.059 0.14 -10000 0 -0.22 214 214
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.064 0.15 0.21 1 -0.23 211 212
RHOC 0.023 0.001 -10000 0 -10000 0 0
XIAP 0.023 0.002 -10000 0 -10000 0 0
MAPK10 -0.14 0.17 0.22 4 -0.33 182 186
DIABLO 0.023 0.003 -10000 0 -10000 0 0
SMPD2 -0.1 0.12 0.18 3 -0.23 209 212
APH1B 0.018 0.04 -10000 0 -0.35 6 6
APH1A 0.019 0.009 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin -0.079 0.16 0.2 1 -0.26 212 213
PSEN1 0.022 0.004 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.033 0.007 -10000 0 -10000 0 0
NT3 (dimer)/p75(NTR) -0.068 0.14 0.21 5 -0.26 178 183
MAPK8 -0.1 0.14 0.22 4 -0.28 161 165
MAPK9 -0.1 0.14 0.22 4 -0.28 161 165
APAF1 0.023 0.002 -10000 0 -10000 0 0
NTF3 0.003 0.091 0.28 5 -0.35 30 35
NTF4 0.031 0.055 0.28 22 -0.35 1 23
NDN -0.15 0.18 -10000 0 -0.35 239 239
RAC1/GDP 0.016 0.003 -10000 0 -10000 0 0
RhoA-B-C/GDP -0.056 0.14 -10000 0 -0.21 217 217
p75 CTF/Sortilin/TRAF6/NRIF 0.053 0.019 -10000 0 -10000 0 0
RhoA-B-C/GTP -0.082 0.16 0.2 1 -0.25 220 221
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0 0.13 -10000 0 -0.18 163 163
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.006 0.14 0.21 67 -0.19 164 231
PRKACB 0.019 0.04 -10000 0 -0.35 6 6
proBDNF (dimer)/p75 ECD 0.058 0.064 0.21 78 -10000 0 78
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 0.018 0.046 0.28 2 -0.35 7 9
BIRC2 0.022 0.004 -10000 0 -10000 0 0
neuron projection morphogenesis -0.17 0.16 0.11 18 -0.3 255 273
BAD -0.12 0.15 0.21 5 -0.31 173 178
RIPK2 0.021 0.007 -10000 0 -10000 0 0
NGFR -0.097 0.17 0.28 1 -0.35 166 167
CYCS -0.095 0.11 0.17 6 -0.22 201 207
ADAM17 0.022 0.005 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/TRAF6/RIP2 -0.062 0.15 0.21 1 -0.23 203 204
BCL2L11 -0.12 0.15 0.21 4 -0.31 175 179
BDNF (dimer)/p75(NTR) -0.035 0.16 0.21 67 -0.24 166 233
PI3K -0.065 0.14 0.21 1 -0.23 208 209
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 -0.064 0.15 0.21 1 -0.23 211 212
NDNL2 0.022 0.005 -10000 0 -10000 0 0
YWHAE 0.021 0.007 -10000 0 -10000 0 0
PRKCI 0.021 0.007 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR) -0.11 0.17 0.21 1 -0.3 217 218
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE -0.063 0.15 0.21 1 -0.23 210 211
TRAF6 0.022 0.005 -10000 0 -10000 0 0
RAC1 0.022 0.005 -10000 0 -10000 0 0
PRKCZ 0.022 0.02 0.28 1 -0.35 1 2
PLG -0.004 0.11 0.28 8 -0.35 41 49
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 -0.088 0.14 0.16 4 -0.25 205 209
SQSTM1 0.022 0.004 -10000 0 -10000 0 0
NGFRAP1 0.019 0.04 -10000 0 -0.35 6 6
CASP3 -0.11 0.15 0.21 4 -0.29 177 181
E2F1 0.072 0.1 0.28 98 -10000 0 98
CASP9 0.022 0.005 -10000 0 -10000 0 0
IKK complex -0.057 0.14 -10000 0 -0.32 88 88
NGF (dimer)/TRKA -0.024 0.11 0.21 5 -0.24 99 104
MMP7 0.027 0.13 0.28 59 -0.35 34 93
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.055 0.15 -10000 0 -0.22 207 207
MMP3 0.066 0.098 0.28 90 -10000 0 90
APAF-1/Caspase 9 -0.093 0.091 -10000 0 -0.29 53 53
FOXM1 transcription factor network

Figure S7.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S7.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC3 0.21 0.4 0.81 69 -0.88 8 77
PLK1 0.19 0.18 0.46 42 -0.63 11 53
BIRC5 0.21 0.16 0.45 46 -0.75 5 51
HSPA1B 0.21 0.4 0.79 79 -0.88 9 88
MAP2K1 0.064 0.085 0.23 64 -10000 0 64
BRCA2 0.2 0.4 0.78 75 -0.94 10 85
FOXM1 0.23 0.45 0.88 81 -0.98 11 92
XRCC1 0.21 0.4 0.8 72 -0.89 8 80
FOXM1B/p19 0.001 0.34 0.71 34 -0.89 17 51
Cyclin D1/CDK4 0.2 0.37 0.71 84 -0.81 9 93
CDC2 0.21 0.42 0.82 84 -0.87 12 96
TGFA 0.2 0.37 0.71 89 -0.78 10 99
SKP2 0.21 0.4 0.79 80 -0.86 9 89
CCNE1 0.14 0.14 0.3 211 -10000 0 211
CKS1B 0.24 0.41 0.82 90 -0.88 7 97
RB1 0.17 0.25 0.52 116 -0.66 5 121
FOXM1C/SP1 0.19 0.4 0.75 67 -0.93 11 78
AURKB 0.18 0.24 0.48 19 -0.74 22 41
CENPF 0.26 0.42 0.84 104 -0.88 8 112
CDK4 0.038 0.038 0.16 2 -10000 0 2
MYC 0.15 0.35 0.7 68 -0.84 9 77
CHEK2 0.064 0.085 0.23 65 -10000 0 65
ONECUT1 0.2 0.38 0.74 82 -0.83 10 92
CDKN2A 0.058 0.14 0.24 188 -0.14 32 220
LAMA4 0.15 0.49 0.79 75 -0.92 42 117
FOXM1B/HNF6 0.2 0.4 0.76 75 -0.93 10 85
FOS -0.012 0.61 0.8 72 -0.98 91 163
SP1 0.022 0.013 -10000 0 -0.15 1 1
CDC25B 0.21 0.4 0.78 81 -0.86 9 90
response to radiation 0.038 0.059 0.16 57 -10000 0 57
CENPB 0.21 0.4 0.8 74 -0.88 8 82
CENPA 0.26 0.42 0.8 109 -0.84 9 118
NEK2 0.28 0.42 0.85 100 -0.89 7 107
HIST1H2BA 0.2 0.4 0.8 70 -0.9 8 78
CCNA2 0.083 0.11 0.3 108 -10000 0 108
EP300 0.021 0.006 -10000 0 -10000 0 0
CCNB1/CDK1 0.2 0.42 0.83 71 -0.95 11 82
CCNB2 0.26 0.42 0.81 100 -0.9 7 107
CCNB1 0.22 0.42 0.83 82 -0.9 10 92
ETV5 0.22 0.41 0.82 80 -0.92 8 88
ESR1 0.14 0.5 0.8 76 -0.96 35 111
CCND1 0.2 0.38 0.74 85 -0.82 9 94
GSK3A 0.052 0.069 0.19 48 -10000 0 48
Cyclin A-E1/CDK1-2 0.16 0.15 0.31 215 -10000 0 215
CDK2 0.029 0.025 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.052 0.076 0.2 77 -10000 0 77
FOXM1B/Cbp/p300 0.14 0.36 0.68 47 -0.91 10 57
GAS1 -0.28 0.62 0.8 67 -0.93 153 220
MMP2 0.17 0.46 0.78 78 -1.1 24 102
RB1/FOXM1C 0.19 0.37 0.71 87 -0.88 8 95
CREBBP 0.022 0.005 -10000 0 -10000 0 0
PDGFR-alpha signaling pathway

Figure S8.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S8.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA -0.094 0.16 -10000 0 -0.36 137 137
PDGF/PDGFRA/CRKL -0.053 0.12 -10000 0 -0.25 135 135
positive regulation of JUN kinase activity -0.003 0.088 -10000 0 -0.19 90 90
CRKL 0.022 0.005 -10000 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 -0.056 0.12 0.19 1 -0.25 135 136
AP1 -0.28 0.36 -10000 0 -0.81 157 157
mol:IP3 -0.085 0.11 -10000 0 -0.27 127 127
PLCG1 -0.085 0.11 -10000 0 -0.27 127 127
PDGF/PDGFRA/alphaV Integrin -0.054 0.12 -10000 0 -0.25 137 137
RAPGEF1 0.022 0.006 -10000 0 -10000 0 0
CRK 0.021 0.006 -10000 0 -10000 0 0
mol:Ca2+ -0.085 0.11 -10000 0 -0.27 127 127
CAV3 0.018 0.012 0.28 1 -10000 0 1
CAV1 -0.041 0.14 -10000 0 -0.35 88 88
SHC/Grb2/SOS1 -0.002 0.089 -10000 0 -0.19 90 90
PDGF/PDGFRA/Shf -0.057 0.12 -10000 0 -0.25 139 139
FOS -0.27 0.36 0.3 1 -0.8 156 157
JUN -0.042 0.042 -10000 0 -0.3 7 7
oligodendrocyte development -0.054 0.12 -10000 0 -0.25 137 137
GRB2 0.022 0.006 -10000 0 -10000 0 0
PIK3R1 0.018 0.037 -10000 0 -0.35 5 5
mol:DAG -0.085 0.11 -10000 0 -0.27 127 127
PDGF/PDGFRA -0.094 0.16 -10000 0 -0.36 137 137
actin cytoskeleton reorganization -0.053 0.12 -10000 0 -0.25 135 135
SRF 0.005 0.02 -10000 0 -10000 0 0
SHC1 0.019 0.009 -10000 0 -10000 0 0
PI3K -0.028 0.1 -10000 0 -0.21 111 111
PDGF/PDGFRA/Crk/C3G -0.035 0.1 -10000 0 -0.2 135 135
JAK1 -0.077 0.1 -10000 0 -0.25 134 134
ELK1/SRF -0.068 0.09 0.16 10 -0.22 118 128
SHB 0.022 0.004 -10000 0 -10000 0 0
SHF 0.018 0.04 -10000 0 -0.35 6 6
CSNK2A1 0.036 0.021 -10000 0 -10000 0 0
GO:0007205 -0.09 0.12 -10000 0 -0.3 128 128
SOS1 0.023 0.003 -10000 0 -10000 0 0
Ras protein signal transduction -0.003 0.088 -10000 0 -0.19 90 90
PDGF/PDGFRA/SHB -0.053 0.12 -10000 0 -0.25 135 135
PDGF/PDGFRA/Caveolin-1 -0.091 0.16 -10000 0 -0.31 169 169
ITGAV 0.023 0.003 -10000 0 -10000 0 0
ELK1 -0.09 0.11 -10000 0 -0.27 124 124
PIK3CA 0.02 0.018 -10000 0 -0.35 1 1
PDGF/PDGFRA/Crk -0.053 0.12 -10000 0 -0.24 135 135
JAK-STAT cascade -0.077 0.1 -10000 0 -0.25 134 134
cell proliferation -0.057 0.12 -10000 0 -0.25 139 139
Signaling events mediated by the Hedgehog family

Figure S9.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S9.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB2 -0.042 0.16 -10000 0 -0.54 31 31
IHH -0.041 0.21 0.31 57 -0.38 121 178
SHH Np/Cholesterol/GAS1 -0.084 0.1 0.23 1 -0.19 254 255
LRPAP1 0.022 0.004 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0.083 0.1 0.18 254 -0.23 1 255
SMO/beta Arrestin2 -0.039 0.16 -10000 0 -0.31 106 106
SMO -0.057 0.16 -10000 0 -0.33 109 109
AKT1 -0.019 0.12 -10000 0 -0.47 21 21
ARRB2 0.021 0.006 -10000 0 -10000 0 0
BOC 0.01 0.066 -10000 0 -0.35 17 17
ADRBK1 0.022 0.004 -10000 0 -10000 0 0
heart looping -0.056 0.15 -10000 0 -0.32 109 109
STIL -0.01 0.12 0.19 56 -0.28 28 84
DHH N/PTCH2 -0.004 0.098 -10000 0 -0.26 65 65
DHH N/PTCH1 -0.043 0.13 -10000 0 -0.24 126 126
PIK3CA 0.02 0.018 -10000 0 -0.35 1 1
DHH -0.007 0.1 -10000 0 -0.35 41 41
PTHLH -0.062 0.19 -10000 0 -0.58 33 33
determination of left/right symmetry -0.056 0.15 -10000 0 -0.32 109 109
PIK3R1 0.018 0.037 -10000 0 -0.35 5 5
skeletal system development -0.061 0.19 -10000 0 -0.57 33 33
IHH N/Hhip -0.004 0.14 0.22 72 -0.23 118 190
DHH N/Hhip 0.017 0.09 0.21 26 -0.24 46 72
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.056 0.15 -10000 0 -0.32 109 109
pancreas development 0.032 0.069 0.28 28 -0.35 5 33
HHAT 0.017 0.033 -10000 0 -0.35 4 4
PI3K 0.026 0.03 -10000 0 -0.24 5 5
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.2 0.18 -10000 0 -0.35 313 313
somite specification -0.056 0.15 -10000 0 -0.32 109 109
SHH Np/Cholesterol/PTCH1 -0.022 0.11 0.24 5 -0.24 49 54
SHH Np/Cholesterol/PTCH2 0.015 0.06 0.22 6 -0.2 27 33
SHH Np/Cholesterol/Megalin 0.079 0.095 0.2 168 -0.18 6 174
SHH 0.004 0.059 0.13 62 -0.25 6 68
catabolic process -0.037 0.13 -10000 0 -0.25 124 124
SMO/Vitamin D3 -0.015 0.15 0.27 12 -0.26 114 126
SHH Np/Cholesterol/Hhip 0.03 0.06 0.21 33 -0.18 11 44
LRP2 0.11 0.12 0.28 179 -10000 0 179
receptor-mediated endocytosis -0.009 0.14 0.23 11 -0.32 32 43
SHH Np/Cholesterol/BOC 0.017 0.054 0.22 6 -0.19 22 28
SHH Np/Cholesterol/CDO 0.005 0.07 0.22 6 -0.19 47 53
mesenchymal cell differentiation -0.03 0.059 0.18 11 -0.2 33 44
mol:Vitamin D3 0 0.14 0.29 16 -0.28 31 47
IHH N/PTCH2 -0.022 0.15 0.2 56 -0.25 130 186
CDON -0.015 0.11 -10000 0 -0.35 52 52
IHH N/PTCH1 -0.026 0.15 -10000 0 -0.25 124 124
Megalin/LRPAP1 0.09 0.084 0.21 172 -10000 0 172
PTCH2 0.002 0.084 -10000 0 -0.35 28 28
SHH Np/Cholesterol 0.008 0.023 -10000 0 -0.18 6 6
PTCH1 -0.037 0.13 -10000 0 -0.25 124 124
HHIP 0.032 0.069 0.28 28 -0.35 5 33
Integrins in angiogenesis

Figure S10.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S10.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer 0.017 0.064 -10000 0 -0.24 29 29
alphaV beta3 Integrin -0.12 0.15 0.2 1 -0.24 285 286
PTK2 -0.1 0.18 0.31 8 -0.37 112 120
IGF1R 0.008 0.07 -10000 0 -0.35 19 19
PI4KB 0.018 0.01 -10000 0 -10000 0 0
MFGE8 0.021 0.023 -10000 0 -0.35 2 2
SRC 0.022 0.005 -10000 0 -10000 0 0
CDKN1B -0.12 0.19 -10000 0 -0.51 89 89
VEGFA 0.023 0.003 -10000 0 -10000 0 0
ILK -0.1 0.17 -10000 0 -0.48 73 73
ROCK1 0.023 0.004 -10000 0 -10000 0 0
AKT1 -0.097 0.16 -10000 0 -0.46 70 70
PTK2B -0.041 0.085 0.2 14 -0.2 85 99
alphaV/beta3 Integrin/JAM-A -0.098 0.14 0.2 3 -0.22 266 269
CBL 0.022 0.005 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 0.001 0.094 0.2 3 -0.21 85 88
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.017 0.13 -10000 0 -0.24 128 128
VEGF/Rho/ROCK/alphaV/beta3 Integrin -0.046 0.11 -10000 0 -0.32 35 35
alphaV/beta3 Integrin/Syndecan-1 0.044 0.13 0.21 130 -0.2 81 211
PI4KA 0.022 0.005 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.14 0.18 -10000 0 -0.26 319 319
PI4 Kinase 0.025 0.015 -10000 0 -10000 0 0
PIK3CA 0.02 0.018 -10000 0 -0.35 1 1
alphaV/beta3 Integrin/Osteopontin 0.04 0.13 0.2 124 -0.2 84 208
RPS6KB1 -0.16 0.14 0.32 1 -0.36 135 136
TLN1 0.022 0.005 -10000 0 -10000 0 0
MAPK3 -0.25 0.25 -10000 0 -0.47 274 274
GPR124 -0.059 0.15 -10000 0 -0.35 111 111
MAPK1 -0.26 0.25 -10000 0 -0.47 276 276
PXN 0.023 0.003 -10000 0 -10000 0 0
PIK3R1 0.018 0.037 -10000 0 -0.35 5 5
alphaV/beta3 Integrin/Tumstatin -0.011 0.12 0.2 18 -0.23 113 131
cell adhesion -0.005 0.097 0.23 2 -0.22 81 83
ANGPTL3 0.021 0.017 0.28 2 -10000 0 2
VEGFR2 homodimer/VEGFA homodimer/Src 0.03 0.057 -10000 0 -0.21 27 27
IGF-1R heterotetramer 0.008 0.07 -10000 0 -0.35 19 19
Rac1/GDP 0.016 0.003 -10000 0 -10000 0 0
TGFBR2 0.014 0.054 -10000 0 -0.35 11 11
ITGB3 -0.038 0.14 0.28 2 -0.35 85 87
IGF1 -0.048 0.15 -10000 0 -0.35 99 99
RAC1 0.022 0.005 -10000 0 -10000 0 0
regulation of cell-matrix adhesion -0.045 0.14 0.2 1 -0.24 155 156
apoptosis 0.023 0.003 -10000 0 -10000 0 0
CD47 0.022 0.004 -10000 0 -10000 0 0
alphaV/beta3 Integrin/CD47 0.003 0.092 0.2 1 -0.21 82 83
VCL 0.022 0.005 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Del1 -0.039 0.14 0.2 2 -0.25 147 149
CSF1 0.016 0.051 -10000 0 -0.35 10 10
PIK3C2A -0.1 0.16 -10000 0 -0.48 71 71
PI4 Kinase/Pyk2 -0.095 0.13 -10000 0 -0.23 197 197
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.004 0.11 0.21 1 -0.21 95 96
FAK1/Vinculin -0.081 0.14 0.28 6 -0.32 95 101
alphaV beta3/Integrin/ppsTEM5 -0.045 0.14 0.2 1 -0.24 155 156
RHOA 0.022 0.005 -10000 0 -10000 0 0
VTN -0.023 0.12 0.3 3 -0.35 63 66
BCAR1 0.02 0.007 -10000 0 -10000 0 0
FGF2 -0.17 0.18 -10000 0 -0.35 265 265
F11R -0.1 0.12 -10000 0 -0.24 210 210
alphaV/beta3 Integrin/Lactadherin 0.002 0.096 0.2 2 -0.21 84 86
alphaV/beta3 Integrin/TGFBR2 -0.001 0.1 0.2 2 -0.22 86 88
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.045 0.04 -10000 0 -0.19 10 10
HSP90AA1 0.022 0.004 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Talin 0.004 0.085 0.19 2 -0.19 84 86
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.019 0.036 -10000 0 -0.35 5 5
alphaV/beta3 Integrin/Pyk2 -0.009 0.094 0.19 1 -0.2 91 92
SDC1 0.096 0.12 0.28 147 -10000 0 147
VAV3 0.026 0.086 0.24 18 -0.18 8 26
PTPN11 0.023 0.003 -10000 0 -10000 0 0
IRS1 -0.013 0.11 -10000 0 -0.35 50 50
FAK1/Paxillin -0.082 0.15 0.3 7 -0.31 102 109
cell migration -0.077 0.13 0.23 14 -0.29 88 102
ITGAV 0.023 0.003 -10000 0 -10000 0 0
PI3K -0.082 0.13 -10000 0 -0.22 208 208
SPP1 0.095 0.12 0.28 146 -10000 0 146
KDR 0.001 0.087 -10000 0 -0.35 30 30
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.023 0.003 -10000 0 -10000 0 0
COL4A3 0 0.12 0.28 19 -0.35 43 62
angiogenesis -0.26 0.26 -10000 0 -0.49 265 265
Rac1/GTP 0.022 0.08 0.23 15 -10000 0 15
EDIL3 -0.047 0.14 -10000 0 -0.35 96 96
cell proliferation -0.001 0.1 0.2 2 -0.22 86 88
HIF-1-alpha transcription factor network

Figure S11.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S11.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PKM2 -0.14 0.31 0.42 3 -0.64 90 93
HDAC7 0.023 0.005 -10000 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.15 0.34 0.57 5 -0.7 92 97
SMAD4 0.023 0.005 -10000 0 -10000 0 0
ID2 -0.14 0.31 0.42 3 -0.65 88 91
AP1 -0.051 0.13 -10000 0 -0.25 154 154
ABCG2 -0.22 0.36 0.43 2 -0.65 162 164
HIF1A -0.031 0.078 -10000 0 -0.21 10 10
TFF3 -0.11 0.36 0.45 35 -0.68 85 120
GATA2 -0.011 0.11 -10000 0 -0.35 47 47
AKT1 -0.047 0.098 -10000 0 -0.22 56 56
response to hypoxia -0.053 0.093 0.15 3 -0.2 98 101
MCL1 -0.15 0.29 0.43 2 -0.64 84 86
NDRG1 -0.14 0.3 0.42 3 -0.64 83 86
SERPINE1 -0.14 0.31 0.42 3 -0.65 89 92
FECH -0.14 0.31 0.42 3 -0.64 90 93
FURIN -0.14 0.31 0.42 3 -0.64 89 92
NCOA2 0.009 0.065 -10000 0 -0.35 16 16
EP300 -0.061 0.14 0.22 2 -0.32 91 93
HMOX1 -0.14 0.31 0.45 4 -0.64 92 96
BHLHE40 -0.14 0.31 0.42 3 -0.65 87 90
BHLHE41 -0.16 0.33 0.42 3 -0.66 106 109
HIF1A/ARNT/SMAD3/SMAD4/SP1 -0.008 0.11 0.32 1 -0.28 2 3
ENG -0.001 0.11 0.3 6 -0.26 2 8
JUN 0.018 0.044 -10000 0 -0.35 7 7
RORA -0.15 0.32 0.42 3 -0.66 94 97
ABCB1 -0.25 0.44 -10000 0 -0.96 136 136
TFRC -0.14 0.31 0.45 4 -0.64 84 88
CXCR4 -0.14 0.31 0.42 3 -0.64 90 93
TF -0.14 0.32 0.46 6 -0.67 85 91
CITED2 -0.15 0.32 0.42 3 -0.66 87 90
HIF1A/ARNT -0.13 0.38 0.67 18 -0.76 72 90
LDHA -0.027 0.12 -10000 0 -0.57 15 15
ETS1 -0.14 0.31 0.42 3 -0.65 88 91
PGK1 -0.14 0.31 0.42 3 -0.65 89 92
NOS2 -0.14 0.31 0.42 3 -0.65 90 93
ITGB2 -0.14 0.31 0.46 5 -0.65 89 94
ALDOA -0.14 0.31 0.42 3 -0.65 87 90
Cbp/p300/CITED2 -0.19 0.38 0.49 3 -0.77 105 108
FOS -0.087 0.17 -10000 0 -0.35 152 152
HK2 -0.14 0.31 0.47 4 -0.65 88 92
SP1 -0.007 0.059 -10000 0 -0.12 55 55
GCK -0.18 0.43 -10000 0 -1.2 75 75
HK1 -0.14 0.31 0.42 3 -0.65 88 91
NPM1 -0.14 0.31 0.42 3 -0.65 87 90
EGLN1 -0.15 0.3 0.43 2 -0.64 85 87
CREB1 0.026 0.003 -10000 0 -10000 0 0
PGM1 -0.14 0.31 0.42 3 -0.64 91 94
SMAD3 0.02 0.033 -10000 0 -0.35 4 4
EDN1 -0.13 0.24 -10000 0 -0.61 71 71
IGFBP1 -0.16 0.34 0.46 6 -0.67 101 107
VEGFA -0.13 0.29 0.44 2 -0.6 91 93
HIF1A/JAB1 -0.01 0.061 -10000 0 -0.19 1 1
CP -0.12 0.33 0.48 11 -0.66 83 94
CXCL12 -0.24 0.36 0.42 3 -0.66 158 161
COPS5 0.02 0.011 -10000 0 -10000 0 0
SMAD3/SMAD4 0.031 0.026 -10000 0 -0.24 4 4
BNIP3 -0.14 0.31 0.42 3 -0.65 87 90
EGLN3 -0.14 0.31 0.5 2 -0.65 89 91
CA9 -0.1 0.34 0.47 27 -0.65 82 109
TERT -0.11 0.33 0.47 22 -0.65 79 101
ENO1 -0.14 0.31 0.42 3 -0.66 84 87
PFKL -0.14 0.31 0.42 3 -0.64 90 93
NCOA1 0.021 0.018 -10000 0 -0.35 1 1
ADM -0.14 0.32 0.46 6 -0.65 85 91
ARNT -0.019 0.064 0.18 1 -10000 0 1
HNF4A 0.045 0.1 0.28 72 -0.14 1 73
ADFP -0.16 0.3 0.38 7 -0.64 93 100
SLC2A1 -0.13 0.29 0.44 3 -0.6 91 94
LEP -0.14 0.31 0.44 4 -0.66 84 88
HIF1A/ARNT/Cbp/p300 -0.16 0.34 0.59 5 -0.71 93 98
EPO -0.1 0.27 0.44 1 -0.74 38 39
CREBBP -0.062 0.14 0.2 1 -0.33 90 91
HIF1A/ARNT/Cbp/p300/HDAC7 -0.14 0.33 0.57 5 -0.69 90 95
PFKFB3 -0.14 0.31 0.42 3 -0.65 87 90
NT5E -0.17 0.34 0.42 3 -0.68 105 108
PLK1 signaling events

Figure S12.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S12.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
regulation of centriole-centriole cohesion -0.056 0.046 0.14 14 -0.11 31 45
BUB1B 0.062 0.064 0.12 150 -0.17 14 164
PLK1 0.035 0.033 0.1 39 -0.1 7 46
PLK1S1 0.021 0.025 0.11 8 -0.18 3 11
KIF2A 0.027 0.031 0.12 14 -0.11 1 15
regulation of mitotic centrosome separation 0.035 0.033 0.1 39 -0.1 7 46
GOLGA2 0.022 0.005 -10000 0 -10000 0 0
Hec1/SPC24 0.16 0.1 0.24 310 -10000 0 310
WEE1 0.023 0.072 0.16 2 -0.29 21 23
cytokinesis 0.094 0.069 0.18 60 -0.22 10 70
PP2A-alpha B56 0.14 0.1 -10000 0 -0.55 8 8
AURKA 0.045 0.051 0.12 130 -0.2 4 134
PICH/PLK1 0.076 0.078 0.17 187 -10000 0 187
CENPE 0.032 0.035 0.13 17 -0.14 3 20
RhoA/GTP 0.016 0.004 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization 0.028 0.031 0.12 14 -0.11 1 15
PPP2CA 0.023 0.003 -10000 0 -10000 0 0
FZR1 0.021 0.006 -10000 0 -10000 0 0
TPX2 0.089 0.047 0.11 333 -0.24 1 334
PAK1 0.021 0.004 -10000 0 -10000 0 0
SPC24 0.18 0.13 0.28 314 -10000 0 314
FBXW11 0.022 0.004 -10000 0 -10000 0 0
CLSPN 0.075 0.064 0.12 245 -0.23 8 253
GORASP1 0.022 0.004 -10000 0 -10000 0 0
metaphase 0 0.002 0.012 6 -0.011 11 17
mol:GTP 0 0 -10000 0 -10000 0 0
NLP 0.016 0.016 0.052 36 -0.051 7 43
G2 phase of mitotic cell cycle 0 0.004 0.014 27 -10000 0 27
STAG2 0.023 0.002 -10000 0 -10000 0 0
GRASP65/GM130/RAB1/GTP 0.006 0.085 -10000 0 -0.51 13 13
spindle elongation 0.035 0.033 0.1 39 -0.1 7 46
ODF2 0.022 0.006 -10000 0 -10000 0 0
BUB1 0.14 0.11 -10000 0 -0.6 8 8
TPT1 0.011 0.051 0.11 3 -0.19 28 31
CDC25C 0.12 0.067 0.15 150 -0.28 10 160
CDC25B 0.023 0.009 -10000 0 -10000 0 0
SGOL1 0.056 0.046 0.11 31 -0.14 14 45
RHOA 0.022 0.005 -10000 0 -10000 0 0
CCNB1/CDK1 0.055 0.064 0.19 76 -0.15 4 80
CDC14B -0.005 0.004 -10000 0 -10000 0 0
CDC20 0.25 0.083 0.28 459 -10000 0 459
PLK1/PBIP1 0.007 0.026 0.099 29 -0.09 6 35
mitosis -0.005 0.007 0.021 4 -0.017 104 108
FBXO5 0.022 0.03 0.14 11 -0.13 3 14
CDC2 0.002 0.004 0.01 57 -0.01 6 63
NDC80 0.042 0.07 0.29 37 -10000 0 37
metaphase plate congression 0.021 0.051 0.14 2 -0.22 17 19
ERCC6L 0.067 0.075 0.18 117 -0.16 2 119
NLP/gamma Tubulin 0.015 0.026 0.074 11 -0.095 14 25
microtubule cytoskeleton organization 0.011 0.05 0.11 3 -0.18 28 31
G2/M transition DNA damage checkpoint -0.001 0.002 0.014 5 -10000 0 5
PPP1R12A 0.023 0.017 -10000 0 -0.35 1 1
interphase -0.001 0.002 0.014 5 -10000 0 5
PLK1/PRC1-2 0.19 0.081 0.22 443 -0.16 1 444
GRASP65/GM130/RAB1/GTP/PLK1 0.056 0.03 -10000 0 -10000 0 0
RAB1A 0.023 0.003 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA 0.027 0.029 0.092 44 -0.084 4 48
mitotic prometaphase 0.001 0.004 0.021 15 -10000 0 15
proteasomal ubiquitin-dependent protein catabolic process 0.051 0.07 0.17 3 -0.34 10 13
microtubule-based process 0.19 0.068 0.22 458 -0.17 1 459
Golgi organization 0.035 0.033 0.1 39 -0.1 7 46
Cohesin/SA2 0.041 0.027 0.11 9 -0.11 2 11
PPP1CB/MYPT1 0.033 0.015 -10000 0 -0.25 1 1
KIF20A 0.25 0.082 0.28 461 -10000 0 461
APC/C/CDC20 0.19 0.07 0.22 458 -0.14 2 460
PPP2R1A 0.022 0.004 -10000 0 -10000 0 0
chromosome segregation 0.006 0.026 0.098 29 -0.089 6 35
PRC1 0.033 0.052 0.28 22 -10000 0 22
ECT2 0.051 0.079 0.25 62 -0.12 1 63
C13orf34 0.027 0.028 0.088 40 -0.086 5 45
NUDC 0.021 0.051 0.14 2 -0.22 17 19
regulation of attachment of spindle microtubules to kinetochore 0.062 0.063 0.12 150 -0.17 14 164
spindle assembly 0.024 0.027 0.087 28 -0.091 7 35
spindle stabilization 0.021 0.025 0.11 8 -0.18 3 11
APC/C/HCDH1 0.018 0.007 -10000 0 -10000 0 0
MKLP2/PLK1 0.19 0.068 0.22 458 -0.17 1 459
CCNB1 0.068 0.098 0.28 90 -10000 0 90
PPP1CB 0.023 0.005 -10000 0 -10000 0 0
BTRC 0.022 0.005 -10000 0 -10000 0 0
ROCK2 0.023 0.068 0.17 5 -0.3 17 22
TUBG1 0.011 0.048 0.12 1 -0.18 27 28
G2/M transition of mitotic cell cycle 0.022 0.038 0.18 7 -0.14 4 11
MLF1IP 0.003 0.026 0.11 31 -10000 0 31
INCENP 0.023 0.004 -10000 0 -10000 0 0
Reelin signaling pathway

Figure S13.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S13.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CDK5R1/CDK5 0.031 0.013 0.21 1 -10000 0 1
VLDLR 0.021 0.024 -10000 0 -0.35 2 2
CRKL 0.022 0.005 -10000 0 -10000 0 0
LRPAP1 0.022 0.004 -10000 0 -10000 0 0
FYN 0.022 0.004 -10000 0 -10000 0 0
ITGA3 0.021 0.017 -10000 0 -0.35 1 1
RELN/VLDLR/Fyn -0.038 0.12 0.2 5 -0.21 166 171
MAPK8IP1/MKK7/MAP3K11/JNK1 0.045 0.04 -10000 0 -0.18 5 5
AKT1 -0.054 0.092 0.15 3 -0.19 165 168
MAP2K7 0.021 0.006 -10000 0 -10000 0 0
RAPGEF1 0.022 0.006 -10000 0 -10000 0 0
DAB1 0.027 0.041 0.28 13 -10000 0 13
RELN/LRP8/DAB1 -0.03 0.12 0.21 19 -0.19 172 191
LRPAP1/LRP8 0.035 0.019 0.21 5 -10000 0 5
RELN/LRP8/DAB1/Fyn -0.019 0.12 0.21 19 -0.18 167 186
DAB1/alpha3/beta1 Integrin -0.025 0.1 -10000 0 -0.18 159 159
long-term memory -0.09 0.15 0.29 4 -0.22 272 276
DAB1/LIS1 -0.02 0.11 -10000 0 -0.18 165 165
DAB1/CRLK/C3G -0.027 0.1 -10000 0 -0.18 163 163
PIK3CA 0.02 0.018 -10000 0 -0.35 1 1
DAB1/NCK2 -0.017 0.12 -10000 0 -0.18 166 166
ARHGEF2 0.018 0.01 -10000 0 -10000 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -10000 0 -10000 0 0
GRIN2A -0.12 0.18 0.28 1 -0.35 193 194
CDK5R1 0.022 0.013 0.28 1 -10000 0 1
RELN -0.1 0.18 0.28 6 -0.35 174 180
PIK3R1 0.018 0.037 -10000 0 -0.35 5 5
RELN/LRP8/Fyn -0.036 0.12 0.23 8 -0.21 167 175
GRIN2A/RELN/LRP8/DAB1/Fyn -0.092 0.15 -10000 0 -0.22 276 276
MAPK8 0.019 0.037 -10000 0 -0.35 5 5
RELN/VLDLR/DAB1 -0.032 0.11 0.2 15 -0.19 170 185
ITGB1 0.022 0.004 -10000 0 -10000 0 0
MAP1B -0.072 0.099 0.18 10 -0.2 181 191
RELN/LRP8 -0.038 0.12 0.23 7 -0.21 171 178
GRIN2B/RELN/LRP8/DAB1/Fyn -0.009 0.13 0.36 6 -0.18 166 172
PI3K 0.026 0.03 -10000 0 -0.24 5 5
mol:PP2 0 0 -10000 0 -10000 0 0
alpha3/beta1 Integrin 0.031 0.015 -10000 0 -0.24 1 1
RAP1A -0.057 0.091 0.3 4 -0.31 1 5
PAFAH1B1 0.021 0.006 -10000 0 -10000 0 0
MAPK8IP1 0.022 0.02 0.28 1 -0.35 1 2
CRLK/C3G 0.031 0.01 -10000 0 -10000 0 0
GRIN2B 0.03 0.053 0.29 21 -10000 0 21
NCK2 0.023 0.003 -10000 0 -10000 0 0
neuron differentiation -0.027 0.092 -10000 0 -0.26 17 17
neuron adhesion -0.053 0.1 0.31 10 -0.3 2 12
LRP8 0.025 0.026 0.29 5 -10000 0 5
GSK3B -0.056 0.086 0.13 3 -0.18 159 162
RELN/VLDLR/DAB1/Fyn -0.022 0.11 0.21 13 -0.18 165 178
MAP3K11 0.022 0.004 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/P13K -0.053 0.1 0.16 4 -0.2 170 174
CDK5 0.022 0.005 -10000 0 -10000 0 0
MAPT -0.003 0.082 0.66 4 -0.31 16 20
neuron migration -0.072 0.13 0.26 11 -0.25 153 164
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.027 0.092 -10000 0 -0.28 15 15
RELN/VLDLR -0.026 0.12 0.21 6 -0.19 168 174
Cellular roles of Anthrax toxin

Figure S14.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S14.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ANTXR1 0.009 0.07 -10000 0 -0.35 19 19
ANTXR2 -0.092 0.17 -10000 0 -0.35 160 160
negative regulation of myeloid dendritic cell antigen processing and presentation -0.017 0.024 -10000 0 -0.051 161 161
monocyte activation -0.007 0.12 -10000 0 -0.37 43 43
MAP2K2 -0.043 0.17 -10000 0 -0.6 42 42
MAP2K1 -0.018 0.022 0.12 1 -0.077 13 14
MAP2K7 -0.017 0.022 0.12 1 -0.076 13 14
MAP2K6 -0.015 0.028 0.19 3 -0.079 11 14
CYAA -0.062 0.085 -10000 0 -0.18 161 161
MAP2K4 -0.017 0.023 -10000 0 -0.083 15 15
IL1B -0.016 0.047 0.17 13 -0.14 25 38
Channel -0.042 0.11 -10000 0 -0.2 161 161
NLRP1 -0.024 0.042 -10000 0 -0.16 34 34
CALM1 0.022 0.004 -10000 0 -10000 0 0
negative regulation of phagocytosis -0.016 0.065 -10000 0 -0.46 9 9
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.017 0.024 0.051 161 -10000 0 161
MAPK3 -0.018 0.022 -10000 0 -0.075 14 14
MAPK1 -0.018 0.021 -10000 0 -0.077 11 11
PGR -0.062 0.08 -10000 0 -0.19 144 144
PA/Cellular Receptors -0.048 0.12 -10000 0 -0.22 161 161
apoptosis -0.017 0.024 -10000 0 -0.051 161 161
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) -0.04 0.1 -10000 0 -0.19 161 161
macrophage activation -0.018 0.025 0.13 5 -10000 0 5
TNF 0.053 0.089 0.28 64 -0.35 2 66
VCAM1 -0.007 0.12 -10000 0 -0.38 42 42
platelet activation -0.016 0.065 -10000 0 -0.46 9 9
MAPKKK cascade 0.015 0.029 0.088 21 -0.078 10 31
IL18 -0.018 0.03 0.11 1 -0.13 16 17
negative regulation of macrophage activation -0.017 0.024 -10000 0 -0.051 161 161
LEF -0.017 0.024 -10000 0 -0.052 161 161
CASP1 -0.018 0.033 -10000 0 -0.062 145 145
mol:cAMP -0.016 0.066 -10000 0 -0.46 9 9
necrosis -0.017 0.024 -10000 0 -0.051 161 161
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) -0.039 0.1 -10000 0 -0.18 161 161
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
Effects of Botulinum toxin

Figure S15.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S15.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
STX1A -0.005 0.013 0.29 1 -10000 0 1
UniProt:P19321 0 0 -10000 0 -10000 0 0
RIMS1/UNC13B 0.032 0.02 0.21 5 -10000 0 5
STXBP1 -0.003 0.093 -10000 0 -0.35 35 35
ACh/CHRNA1 0.043 0.11 0.18 181 -0.13 13 194
RAB3GAP2/RIMS1/UNC13B 0.037 0.024 0.21 4 -10000 0 4
mol:Ca2+ 0 0 -10000 0 -10000 0 0
UniProt:P30996 0 0 -10000 0 -10000 0 0
UniProt:Q60393 0 0 -10000 0 -10000 0 0
CST086 0 0 -10000 0 -10000 0 0
RIMS1 0.023 0.027 0.29 5 -10000 0 5
mol:ACh -0.047 0.058 0.083 20 -0.1 236 256
RAB3GAP2 0.019 0.009 -10000 0 -10000 0 0
STX1A/SNAP25/VAMP2 -0.045 0.094 -10000 0 -0.16 177 177
UniProt:P10844 0 0 -10000 0 -10000 0 0
muscle contraction 0.043 0.11 0.18 181 -0.13 13 194
UNC13B 0.022 0.005 -10000 0 -10000 0 0
CHRNA1 0.11 0.12 0.28 184 -10000 0 184
UniProt:P10845 0 0 -10000 0 -10000 0 0
ACh/Synaptotagmin 1 -0.074 0.11 -10000 0 -0.25 124 124
SNAP25 -0.1 0.12 -10000 0 -0.23 239 239
VAMP2 0.003 0.001 -10000 0 -10000 0 0
SYT1 -0.06 0.16 -10000 0 -0.35 115 115
UniProt:Q00496 0 0 -10000 0 -10000 0 0
STXIA/STXBP1 0.004 0.057 0.22 1 -0.2 35 36
STX1A/SNAP25 fragment 1/VAMP2 -0.045 0.094 -10000 0 -0.16 177 177
S1P3 pathway

Figure S16.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S16.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.009 0.07 -10000 0 -0.35 19 19
mol:S1P -0.009 0.013 -10000 0 -10000 0 0
S1P1/S1P/Gi -0.083 0.12 -10000 0 -0.24 160 160
GNAO1 -0.081 0.16 -10000 0 -0.36 120 120
S1P/S1P3/G12/G13 0.006 0.054 -10000 0 -0.2 16 16
AKT1 -0.065 0.17 -10000 0 -0.68 30 30
AKT3 -0.39 0.5 -10000 0 -1 199 199
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.009 0.07 -10000 0 -0.35 19 19
GNAI2 -0.001 0.031 -10000 0 -10000 0 0
GNAI3 0.002 0.029 -10000 0 -10000 0 0
GNAI1 -0.003 0.053 -10000 0 -0.36 8 8
mol:GDP 0 0 -10000 0 -10000 0 0
S1PR3 -0.012 0.072 -10000 0 -0.36 17 17
S1PR2 0.021 0.006 -10000 0 -10000 0 0
EDG1 0 0 -10000 0 -10000 0 0
mol:Ca2+ -0.14 0.19 -10000 0 -0.33 227 227
MAPK3 -0.13 0.18 -10000 0 -0.32 220 220
MAPK1 -0.13 0.18 -10000 0 -0.34 184 184
JAK2 -0.14 0.2 -10000 0 -0.36 192 192
CXCR4 -0.14 0.18 -10000 0 -0.32 227 227
FLT1 -0.003 0.036 -10000 0 -10000 0 0
RhoA/GDP 0.016 0.004 -10000 0 -10000 0 0
Rac1/GDP 0.016 0.003 -10000 0 -10000 0 0
SRC -0.13 0.18 -10000 0 -0.34 185 185
S1P/S1P3/Gi -0.14 0.19 -10000 0 -0.33 227 227
RAC1 0.022 0.005 -10000 0 -10000 0 0
RhoA/GTP -0.13 0.18 -10000 0 -0.33 201 201
VEGFA -0.003 0.035 -10000 0 -10000 0 0
S1P/S1P2/Gi -0.083 0.13 -10000 0 -0.26 157 157
VEGFR1 homodimer/VEGFA homodimer -0.003 0.053 -10000 0 -10000 0 0
RHOA 0.022 0.005 -10000 0 -10000 0 0
S1P/S1P3/Gq -0.024 0.093 -10000 0 -0.26 60 60
GNAQ 0.021 0.017 -10000 0 -0.35 1 1
GNAZ -0.008 0.065 -10000 0 -0.35 15 15
G12/G13 0.031 0.01 -10000 0 -10000 0 0
GNA14 -0.01 0.1 -10000 0 -0.35 44 44
GNA15 0.025 0.03 0.28 7 -10000 0 7
GNA12 0.022 0.005 -10000 0 -10000 0 0
GNA13 0.022 0.005 -10000 0 -10000 0 0
GNA11 0.015 0.049 -10000 0 -0.35 9 9
Rac1/GTP -0.13 0.18 -10000 0 -0.33 201 201
Nongenotropic Androgen signaling

Figure S17.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S17.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 -0.006 0.002 -10000 0 -10000 0 0
GNB1/GNG2 0 0.089 -10000 0 -0.19 93 93
regulation of S phase of mitotic cell cycle -0.014 0.073 -10000 0 -0.2 64 64
GNAO1 -0.066 0.16 -10000 0 -0.35 120 120
HRAS 0.02 0.007 -10000 0 -10000 0 0
SHBG/T-DHT 0.013 0.019 -10000 0 -0.2 4 4
PELP1 0.02 0.008 -10000 0 -10000 0 0
AKT1 -0.005 0.002 -10000 0 -10000 0 0
MAP2K1 -0.061 0.084 0.18 13 -0.26 27 40
T-DHT/AR -0.032 0.095 -10000 0 -0.24 87 87
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP -0.002 0.003 -10000 0 -0.006 154 154
GNAI2 0.022 0.005 -10000 0 -10000 0 0
GNAI3 0.023 0.002 -10000 0 -10000 0 0
GNAI1 0.017 0.046 -10000 0 -0.35 8 8
mol:GDP -0.054 0.11 -10000 0 -0.3 84 84
cell proliferation -0.14 0.2 0.26 2 -0.41 161 163
PIK3CA 0.02 0.018 -10000 0 -0.35 1 1
FOS -0.23 0.34 -10000 0 -0.74 158 158
mol:Ca2+ -0.02 0.029 -10000 0 -0.061 142 142
MAPK3 -0.11 0.15 0.26 2 -0.31 149 151
MAPK1 -0.082 0.14 0.2 1 -0.36 52 53
PIK3R1 0.018 0.037 -10000 0 -0.35 5 5
mol:IP3 -0.001 0.002 -10000 0 -0.004 154 154
cAMP biosynthetic process 0.004 0.025 -10000 0 -0.16 4 4
GNG2 0.017 0.05 0.28 1 -0.35 9 10
potassium channel inhibitor activity -0.001 0.002 -10000 0 -0.004 154 154
HRAS/GTP -0.018 0.082 -10000 0 -0.18 76 76
actin cytoskeleton reorganization 0.027 0.024 -10000 0 -0.16 5 5
SRC 0.021 0.007 -10000 0 -10000 0 0
voltage-gated calcium channel activity -0.001 0.002 -10000 0 -0.004 154 154
PI3K 0.024 0.025 -10000 0 -0.2 5 5
apoptosis 0.14 0.2 0.42 157 -0.26 1 158
T-DHT/AR/PELP1 -0.019 0.085 -10000 0 -0.21 85 85
HRAS/GDP -0.043 0.11 -10000 0 -0.29 84 84
CREB1 -0.15 0.22 0.27 1 -0.45 157 158
RAC1-CDC42/GTP 0.034 0.027 -10000 0 -0.16 5 5
AR -0.042 0.14 -10000 0 -0.35 87 87
GNB1 0.022 0.004 -10000 0 -10000 0 0
RAF1 -0.05 0.079 0.19 16 -0.19 71 87
RAC1-CDC42/GDP -0.022 0.12 -10000 0 -0.28 79 79
T-DHT/AR/PELP1/Src -0.011 0.081 -10000 0 -0.19 76 76
MAP2K2 -0.061 0.083 0.18 11 -0.26 26 37
T-DHT/AR/PELP1/Src/PI3K -0.014 0.073 -10000 0 -0.2 64 64
GNAZ 0.011 0.062 -10000 0 -0.35 15 15
SHBG 0.018 0.033 -10000 0 -0.35 4 4
Gi family/GNB1/GNG2/GDP -0.098 0.17 -10000 0 -0.34 144 144
mol:T-DHT -0.001 0.001 0.002 1 -0.002 93 94
RAC1 0.022 0.005 -10000 0 -10000 0 0
GNRH1 -0.007 0.021 -10000 0 -0.24 4 4
Gi family/GTP -0.06 0.11 -10000 0 -0.21 132 132
CDC42 0.022 0.004 -10000 0 -10000 0 0
Aurora A signaling

Figure S18.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S18.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Aurora A/GADD45A 0.002 0.053 0.21 1 -10000 0 1
BIRC5 0.22 0.11 0.28 397 -10000 0 397
NFKBIA -0.006 0.055 0.32 6 -10000 0 6
CPEB1 -0.14 0.18 -10000 0 -0.35 220 220
AKT1 -0.007 0.054 0.32 5 -10000 0 5
NDEL1 0.021 0.007 -10000 0 -10000 0 0
Aurora A/BRCA1 0 0.045 -10000 0 -0.16 1 1
NDEL1/TACC3 0.037 0.09 0.22 66 -10000 0 66
GADD45A 0.023 0.002 -10000 0 -10000 0 0
GSK3B -0.022 0.024 -10000 0 -10000 0 0
PAK1/Aurora A 0.002 0.052 0.21 1 -10000 0 1
MDM2 0.023 0.002 -10000 0 -10000 0 0
JUB 0 0 -10000 0 -10000 0 0
TPX2 0.097 0.075 0.12 414 -10000 0 414
TP53 0 0.052 -10000 0 -0.2 22 22
DLG7 -0.004 0.044 0.14 25 -10000 0 25
AURKAIP1 0.022 0.004 -10000 0 -10000 0 0
ARHGEF7 0.022 0.005 -10000 0 -10000 0 0
G2 phase of mitotic cell cycle 0 0 -10000 0 -10000 0 0
Aurora A/NDEL1/TACC3 0.039 0.096 0.24 66 -10000 0 66
G2/M transition of mitotic cell cycle 0 0.044 -10000 0 -0.16 1 1
AURKA 0.001 0.062 0.18 26 -10000 0 26
AURKB 0.12 0.074 0.16 361 -0.3 3 364
CDC25B 0.004 0.044 0.21 1 -0.17 2 3
G2/M transition checkpoint -0.008 0.031 0.12 1 -0.13 3 4
mRNA polyadenylation -0.078 0.1 -10000 0 -0.19 202 202
Aurora A/CPEB -0.078 0.1 -10000 0 -0.2 202 202
Aurora A/TACC1/TRAP/chTOG -0.019 0.086 -10000 0 -0.2 52 52
BRCA1 0.022 0.005 -10000 0 -10000 0 0
centrosome duplication 0.002 0.052 0.21 1 -10000 0 1
regulation of centrosome cycle 0.036 0.088 0.22 66 -10000 0 66
spindle assembly -0.02 0.084 -10000 0 -0.2 52 52
TDRD7 0.022 0.006 -10000 0 -10000 0 0
Aurora A/RasGAP/Survivin 0.13 0.095 0.23 143 -0.18 4 147
CENPA 0.13 0.072 0.17 359 -0.29 3 362
Aurora A/PP2A 0.002 0.053 0.21 1 -0.18 1 2
meiosis 0 0 -10000 0 -10000 0 0
protein catabolic process 0.003 0.05 0.25 8 -0.17 1 9
negative regulation of DNA binding 0 0.053 -10000 0 -0.2 23 23
prophase 0 0 -10000 0 -10000 0 0
GIT1/beta-PIX 0.031 0.01 -10000 0 -10000 0 0
RASA1 0.019 0.037 -10000 0 -0.35 5 5
Ajuba/Aurora A -0.008 0.032 0.12 1 -0.13 3 4
mitotic prometaphase -0.024 0.031 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.001 0.062 0.18 26 -10000 0 26
TACC1 -0.04 0.14 -10000 0 -0.35 84 84
TACC3 0.084 0.11 0.29 122 -10000 0 122
Aurora A/Antizyme1 0.006 0.053 -10000 0 -10000 0 0
Aurora A/RasGAP 0 0.056 0.21 1 -0.23 5 6
OAZ1 0.021 0.006 -10000 0 -10000 0 0
RAN 0.023 0.003 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
PRKACA -0.022 0.024 -10000 0 -10000 0 0
GIT1 0.022 0.005 -10000 0 -10000 0 0
GIT1/beta-PIX/PAK1 0.042 0.014 -10000 0 -10000 0 0
Importin alpha/Importin beta/TPX2 0.097 0.075 0.12 414 -10000 0 414
PPP2R5D 0.023 0.004 -10000 0 -10000 0 0
Aurora A/TPX2 0.076 0.073 0.23 56 -10000 0 56
PAK1 0.022 0.004 -10000 0 -10000 0 0
CKAP5 0.022 0.005 -10000 0 -10000 0 0
IGF1 pathway

Figure S19.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S19.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NCK2 0.023 0.003 -10000 0 -10000 0 0
PTK2 0.021 0.007 -10000 0 -10000 0 0
CRKL -0.056 0.096 0.16 1 -0.24 100 101
GRB2/SOS1/SHC 0.035 0.021 -10000 0 -10000 0 0
HRAS 0.022 0.005 -10000 0 -10000 0 0
IRS1/Crk -0.037 0.11 -10000 0 -0.24 102 102
IGF-1R heterotetramer/IGF1/PTP1B -0.01 0.11 -10000 0 -0.23 96 96
AKT1 -0.041 0.1 0.16 32 -0.22 82 114
BAD -0.041 0.094 0.15 32 -0.29 32 64
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.055 0.096 0.16 1 -0.24 96 97
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.033 0.11 0.2 1 -0.21 128 129
RAF1 -0.028 0.1 0.28 2 -0.4 14 16
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos -0.011 0.12 -10000 0 -0.22 102 102
YWHAZ 0.021 0.007 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.034 0.12 -10000 0 -0.23 128 128
PIK3CA 0.02 0.018 -10000 0 -0.35 1 1
RPS6KB1 -0.042 0.097 0.16 29 -0.22 80 109
GNB2L1 0.022 0.004 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade -0.019 0.096 0.26 8 -0.33 9 17
PXN 0.023 0.003 -10000 0 -10000 0 0
PIK3R1 0.018 0.037 -10000 0 -0.35 5 5
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0.031 0.01 -10000 0 -10000 0 0
HRAS/GTP -0.021 0.088 -10000 0 -0.21 77 77
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc 0.012 0.091 -10000 0 -0.19 76 76
IGF-1R heterotetramer -0.01 0.085 -10000 0 -0.4 19 19
IGF-1R heterotetramer/IGF1/IRS/Nck -0.022 0.12 -10000 0 -0.24 107 107
Crk/p130 Cas/Paxillin -0.014 0.11 0.2 1 -0.22 100 101
IGF1R -0.01 0.085 -10000 0 -0.4 19 19
IGF1 -0.057 0.16 -10000 0 -0.38 98 98
IRS2/Crk -0.057 0.12 0.15 1 -0.23 149 150
PI3K -0.011 0.11 -10000 0 -0.23 96 96
apoptosis 0.034 0.085 0.26 30 -0.22 2 32
HRAS/GDP 0.016 0.004 -10000 0 -10000 0 0
PRKCD -0.058 0.14 -10000 0 -0.32 102 102
RAF1/14-3-3 E -0.011 0.1 0.28 2 -0.34 16 18
BAD/14-3-3 -0.036 0.089 0.22 2 -0.28 30 32
PRKCZ -0.039 0.1 0.16 34 -0.22 80 114
Crk/p130 Cas/Paxillin/FAK1 -0.015 0.091 -10000 0 -0.29 30 30
PTPN1 0.022 0.006 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.061 0.14 -10000 0 -0.33 106 106
BCAR1 0.02 0.007 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/SHC/GRB10 0.005 0.094 -10000 0 -0.2 79 79
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.023 0.003 -10000 0 -10000 0 0
IRS1/NCK2 -0.034 0.11 -10000 0 -0.23 107 107
GRB10 0.022 0.017 -10000 0 -0.35 1 1
PTPN11 -0.06 0.097 0.16 1 -0.23 107 108
IRS1 -0.042 0.11 0.12 5 -0.25 104 109
IRS2 -0.078 0.12 0.16 1 -0.24 150 151
IGF-1R heterotetramer/IGF1 -0.039 0.14 -10000 0 -0.3 106 106
GRB2 0.022 0.006 -10000 0 -10000 0 0
PDPK1 -0.041 0.1 0.17 32 -0.23 83 115
YWHAE 0.021 0.007 -10000 0 -10000 0 0
PRKD1 -0.071 0.15 -10000 0 -0.33 110 110
SHC1 0.019 0.009 -10000 0 -10000 0 0
Fc-epsilon receptor I signaling in mast cells

Figure S20.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S20.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PPAP2A 0.021 0.024 -10000 0 -0.35 2 2
LAT2 -0.061 0.12 0.21 1 -0.25 114 115
AP1 -0.084 0.17 -10000 0 -0.38 74 74
mol:PIP3 -0.046 0.17 0.33 16 -0.29 109 125
IKBKB -0.018 0.12 0.24 33 -0.22 45 78
AKT1 -0.001 0.16 0.3 72 -0.28 23 95
IKBKG -0.028 0.12 0.2 50 -0.22 49 99
MS4A2 -0.096 0.16 -10000 0 -0.34 159 159
mol:Sphingosine-1-phosphate 0 0 -10000 0 -10000 0 0
PIK3CA 0.019 0.018 -10000 0 -0.35 1 1
MAP3K1 -0.025 0.14 0.26 30 -0.31 35 65
mol:Ca2+ -0.033 0.14 0.22 53 -0.28 39 92
LYN 0.022 0.01 -10000 0 -10000 0 0
CBLB -0.062 0.12 0.2 1 -0.25 115 116
SHC1 0.019 0.009 -10000 0 -10000 0 0
RasGAP/p62DOK -0.013 0.1 -10000 0 -0.19 120 120
positive regulation of cell migration 0 0 -10000 0 -10000 0 0
INPP5D 0.022 0.017 -10000 0 -0.35 1 1
PLD2 -0.013 0.16 0.28 90 -0.23 57 147
PTPN13 -0.075 0.16 -10000 0 -0.56 14 14
PTPN11 0.019 0.02 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
regulation of mast cell degranulation -0.018 0.14 0.33 18 -0.28 26 44
SYK 0.024 0.014 0.28 1 -10000 0 1
GRB2 0.021 0.006 -10000 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.069 0.13 -10000 0 -0.28 113 113
LAT -0.061 0.11 -10000 0 -0.25 114 114
PAK2 -0.028 0.15 0.26 29 -0.33 39 68
NFATC2 -0.056 0.14 -10000 0 -0.48 44 44
HRAS -0.04 0.15 0.24 11 -0.34 40 51
GAB2 0.02 0.033 -10000 0 -0.35 4 4
PLA2G1B -0.01 0.14 -10000 0 -0.88 12 12
Fc epsilon R1 -0.049 0.13 0.2 1 -0.22 168 169
Antigen/IgE/Fc epsilon R1 -0.042 0.11 0.19 1 -0.2 167 168
mol:GDP -0.061 0.13 -10000 0 -0.36 38 38
JUN 0.018 0.043 -10000 0 -0.35 7 7
mol:Ca++ 0 0 -10000 0 -10000 0 0
PIK3R1 0.018 0.037 -10000 0 -0.35 5 5
FOS -0.087 0.17 -10000 0 -0.35 152 152
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.061 0.12 -10000 0 -0.26 118 118
CHUK -0.028 0.12 0.32 14 -0.22 45 59
KLRG1 -0.051 0.1 0.15 1 -0.21 108 109
VAV1 -0.058 0.11 0.21 1 -0.25 106 107
calcium-dependent protein kinase C activity 0 0 -10000 0 -10000 0 0
CBL -0.059 0.11 0.2 1 -0.25 110 111
negative regulation of mast cell degranulation -0.033 0.11 0.25 1 -0.29 34 35
BTK -0.062 0.13 -10000 0 -0.37 38 38
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.064 0.12 -10000 0 -0.28 87 87
GAB2/PI3K/SHP2 -0.061 0.077 -10000 0 -0.23 58 58
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.051 0.1 -10000 0 -0.26 66 66
RAF1 -0.007 0.15 -10000 0 -0.95 12 12
Fc epsilon R1/FcgammaRIIB/SHIP -0.029 0.12 -10000 0 -0.19 163 163
FCER1G 0.022 0.025 0.29 2 -10000 0 2
FCER1A -0.034 0.13 -10000 0 -0.36 67 67
Antigen/IgE/Fc epsilon R1/Fyn -0.032 0.11 0.2 1 -0.19 162 163
MAPK3 -0.01 0.14 -10000 0 -0.88 12 12
MAPK1 -0.013 0.14 -10000 0 -0.9 12 12
NFKB1 0.022 0.017 -10000 0 -0.35 1 1
MAPK8 -0.052 0.2 -10000 0 -0.55 63 63
DUSP1 -0.064 0.16 -10000 0 -0.35 121 121
NF-kappa-B/RelA -0.016 0.067 0.12 5 -0.14 36 41
actin cytoskeleton reorganization -0.058 0.16 -10000 0 -0.58 10 10
mol:Glucocorticoid Dexamethasone 0 0 -10000 0 -10000 0 0
PI3K -0.042 0.13 -10000 0 -0.34 37 37
FER -0.061 0.11 0.2 1 -0.25 114 115
RELA 0.022 0.004 -10000 0 -10000 0 0
ITK -0.02 0.059 -10000 0 -0.32 14 14
SOS1 0.023 0.003 -10000 0 -10000 0 0
PLCG1 -0.05 0.15 0.27 7 -0.37 37 44
cytokine secretion -0.019 0.041 -10000 0 -10000 0 0
SPHK1 -0.06 0.11 0.2 1 -0.25 111 112
PTK2 -0.061 0.16 -10000 0 -0.64 9 9
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.069 0.14 -10000 0 -0.29 113 113
EDG1 0 0 -10000 0 -10000 0 0
mol:DAG -0.048 0.17 0.33 15 -0.36 43 58
MAP2K2 -0.012 0.14 -10000 0 -0.88 12 12
MAP2K1 -0.012 0.14 -10000 0 -0.89 12 12
MAP2K7 0.021 0.006 -10000 0 -10000 0 0
KLRG1/SHP2 -0.037 0.093 0.21 3 -0.26 38 41
MAP2K4 -0.086 0.32 -10000 0 -0.9 65 65
Fc epsilon R1/FcgammaRIIB -0.037 0.12 0.21 1 -0.2 167 168
mol:Choline -0.013 0.16 0.27 90 -0.23 57 147
SHC/Grb2/SOS1 -0.041 0.12 -10000 0 -0.32 35 35
FYN 0.022 0.004 -10000 0 -10000 0 0
DOK1 0.023 0.003 -10000 0 -10000 0 0
PXN -0.057 0.15 0.31 1 -0.58 9 10
HCLS1 -0.061 0.11 0.2 1 -0.25 113 114
PRKCB -0.042 0.14 0.32 13 -0.29 51 64
FCGR2B 0.018 0.027 0.28 1 -0.35 2 3
IGHE 0 0.007 -10000 0 -10000 0 0
KLRG1/SHIP -0.032 0.12 0.25 1 -0.29 34 35
LCP2 0.023 0.012 0.28 1 -10000 0 1
PLA2G4A -0.067 0.12 0.2 1 -0.25 120 121
RASA1 0.019 0.037 -10000 0 -0.35 5 5
mol:Phosphatidic acid -0.013 0.16 0.27 90 -0.23 57 147
IKK complex -0.007 0.11 0.25 37 -0.18 31 68
WIPF1 0.021 0.023 -10000 0 -0.35 2 2
Wnt signaling

Figure S21.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S21.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Noncanonical Wnts/FZD -0.047 0.14 -10000 0 -0.25 128 128
FZD6 0.02 0.018 -10000 0 -0.35 1 1
WNT6 0.009 0.11 0.28 22 -0.35 34 56
WNT4 -0.066 0.16 -10000 0 -0.35 123 123
FZD3 0.02 0.008 -10000 0 -10000 0 0
WNT5A 0.011 0.064 -10000 0 -0.35 16 16
WNT11 0.035 0.098 0.28 46 -0.35 14 60
TCGA08_retinoblastoma

Figure S22.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S22.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CDKN2B 0.018 0.046 0.29 9 -10000 0 9
CDKN2C 0.021 0.05 -10000 0 -0.34 9 9
CDKN2A 0.13 0.13 0.28 207 -10000 0 207
CCND2 -0.039 0.069 0.14 1 -0.18 55 56
RB1 0.036 0.07 0.22 30 -0.14 2 32
CDK4 -0.036 0.071 0.11 6 -0.33 15 21
CDK6 -0.04 0.076 0.16 1 -0.18 60 61
G1/S progression -0.036 0.074 0.16 5 -0.33 16 21
FOXA2 and FOXA3 transcription factor networks

Figure S23.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S23.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ACADVL -0.084 0.26 0.49 6 -0.61 53 59
PCK1 -0.063 0.32 0.46 10 -1.1 35 45
HNF4A -0.093 0.35 0.67 13 -0.77 67 80
KCNJ11 -0.073 0.27 0.58 6 -0.65 40 46
AKT1 -0.026 0.17 0.4 10 -0.36 23 33
response to starvation -0.005 0.035 -10000 0 -0.17 5 5
DLK1 -0.11 0.34 0.6 9 -0.78 74 83
NKX2-1 -0.056 0.17 0.49 3 -0.55 1 4
ACADM -0.087 0.27 0.49 6 -0.6 60 66
TAT -0.076 0.23 0.49 4 -0.57 45 49
CEBPB 0.023 0.008 -10000 0 -10000 0 0
CEBPA 0.022 0.034 0.28 2 -0.35 3 5
TTR 0.07 0.18 0.55 11 -0.67 8 19
PKLR -0.045 0.28 0.53 19 -0.62 36 55
APOA1 -0.15 0.44 0.67 11 -1 73 84
CPT1C -0.087 0.27 0.49 6 -0.63 56 62
ALAS1 -0.039 0.17 0.47 3 -0.55 6 9
TFRC -0.004 0.21 0.55 11 -0.55 12 23
FOXF1 0.008 0.046 -10000 0 -0.37 5 5
NF1 0.024 0.007 -10000 0 -10000 0 0
HNF1A (dimer) 0.04 0.043 0.29 10 -10000 0 10
CPT1A -0.082 0.26 0.48 7 -0.62 48 55
HMGCS1 -0.079 0.27 0.49 9 -0.6 54 63
NR3C1 -0.053 0.15 -10000 0 -0.29 134 134
CPT1B -0.081 0.26 0.55 6 -0.6 54 60
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 0.034 0.024 -10000 0 -10000 0 0
GCK -0.14 0.35 0.56 6 -0.72 103 109
CREB1 0.017 0.055 -10000 0 -0.18 33 33
IGFBP1 -0.19 0.43 0.52 4 -1.1 85 89
PDX1 -0.001 0.18 0.55 7 -0.56 3 10
UCP2 -0.081 0.27 0.52 8 -0.6 54 62
ALDOB -0.07 0.27 0.58 7 -0.64 40 47
AFP 0.064 0.072 0.36 4 -0.37 1 5
BDH1 -0.068 0.27 0.54 10 -0.6 52 62
HADH -0.071 0.26 0.54 5 -0.64 40 45
F2 -0.09 0.34 0.69 13 -0.78 43 56
HNF1A 0.04 0.043 0.29 10 -10000 0 10
G6PC 0.028 0.071 0.4 1 -10000 0 1
SLC2A2 -0.019 0.19 0.61 5 -0.44 4 9
INS 0.005 0.067 0.19 43 -10000 0 43
FOXA1 0.18 0.14 0.28 323 -0.28 8 331
FOXA3 0.076 0.13 0.31 99 -0.24 14 113
FOXA2 -0.068 0.33 0.7 13 -0.69 50 63
ABCC8 -0.15 0.38 0.6 5 -0.8 102 107
ALB 0.057 0.12 0.34 5 -0.75 9 14
TCGA08_p53

Figure S24.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S24.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CDKN2A 0.042 0.063 0.11 207 -10000 0 207
TP53 0.004 0.046 0.11 2 -0.15 39 41
Senescence 0.004 0.046 0.11 2 -0.15 39 41
Apoptosis 0.004 0.046 0.11 2 -0.15 39 41
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 -0.033 0.048 0.27 5 -0.2 8 13
MDM4 0.019 0.009 -10000 0 -10000 0 0
Signaling mediated by p38-alpha and p38-beta

Figure S25.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S25.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTGS2 -0.075 0.28 0.35 4 -0.85 56 60
MKNK1 0.023 0.004 -10000 0 -10000 0 0
MAPK14 -0.004 0.1 -10000 0 -0.28 59 59
ATF2/c-Jun -0.025 0.1 -10000 0 -0.37 20 20
MAPK11 -0.005 0.1 -10000 0 -0.3 55 55
MITF -0.039 0.15 -10000 0 -0.34 86 86
MAPKAPK5 -0.018 0.12 -10000 0 -0.33 59 59
KRT8 -0.009 0.12 0.26 1 -0.33 59 60
MAPKAPK3 0.022 0.005 -10000 0 -10000 0 0
MAPKAPK2 0.02 0.008 -10000 0 -10000 0 0
p38alpha-beta/CK2 -0.009 0.15 -10000 0 -0.4 60 60
CEBPB -0.014 0.11 0.25 1 -0.33 54 55
SLC9A1 -0.017 0.11 -10000 0 -0.33 58 58
mol:GDP 0 0 -10000 0 -10000 0 0
ATF2 -0.018 0.12 -10000 0 -0.33 61 61
p38alpha-beta/MNK1 0.009 0.12 -10000 0 -0.35 48 48
JUN -0.026 0.1 -10000 0 -0.37 20 20
PPARGC1A -0.07 0.16 -10000 0 -0.32 135 135
USF1 -0.014 0.11 0.28 5 -0.32 53 58
RAB5/GDP/GDI1 -0.012 0.089 -10000 0 -0.25 54 54
NOS2 -0.018 0.14 -10000 0 -0.41 47 47
DDIT3 -0.018 0.12 -10000 0 -0.33 60 60
RAB5A 0.022 0.004 -10000 0 -10000 0 0
HSPB1 -0.017 0.095 0.28 6 -0.27 56 62
p38alpha-beta/HBP1 0.006 0.12 -10000 0 -0.34 49 49
CREB1 -0.02 0.12 -10000 0 -0.36 58 58
RAB5/GDP 0.017 0.003 -10000 0 -10000 0 0
EIF4E -0.017 0.1 0.19 2 -0.31 47 49
RPS6KA4 -0.018 0.12 -10000 0 -0.33 59 59
PLA2G4A -0.024 0.11 0.25 2 -0.32 52 54
GDI1 -0.017 0.11 -10000 0 -0.33 58 58
TP53 -0.029 0.13 -10000 0 -0.41 52 52
RPS6KA5 -0.018 0.12 -10000 0 -0.33 60 60
ESR1 -0.04 0.15 -10000 0 -0.35 84 84
HBP1 0.022 0.004 -10000 0 -10000 0 0
MEF2C -0.038 0.15 -10000 0 -0.35 85 85
MEF2A -0.021 0.12 -10000 0 -0.33 64 64
EIF4EBP1 -0.02 0.12 -10000 0 -0.36 57 57
KRT19 -0.015 0.12 -10000 0 -0.33 56 56
ELK4 -0.015 0.11 0.27 6 -0.32 55 61
ATF6 -0.014 0.11 0.28 5 -0.32 53 58
ATF1 -0.019 0.12 -10000 0 -0.35 58 58
p38alpha-beta/MAPKAPK2 0.002 0.12 -10000 0 -0.33 48 48
p38alpha-beta/MAPKAPK3 0.007 0.12 -10000 0 -0.34 48 48
Neurotrophic factor-mediated Trk receptor signaling

Figure S26.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S26.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CRKL 0.022 0.005 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 -0.058 0.082 -10000 0 -0.23 39 39
NT3 (dimer)/TRKC -0.11 0.15 0.21 3 -0.26 245 248
NT3 (dimer)/TRKB -0.067 0.15 0.2 7 -0.24 202 209
SHC/Grb2/SOS1/GAB1/PI3K 0.01 0.03 -10000 0 -0.19 4 4
RAPGEF1 0.022 0.006 -10000 0 -10000 0 0
BDNF 0.061 0.093 0.28 79 -10000 0 79
PIK3CA 0.02 0.018 -10000 0 -0.35 1 1
DYNLT1 0.022 0.004 -10000 0 -10000 0 0
NTRK1 0.019 0.045 0.28 7 -0.35 4 11
NTRK2 -0.01 0.12 0.28 8 -0.35 50 58
NTRK3 -0.15 0.18 -10000 0 -0.35 243 243
NT-4/5 (dimer)/TRKB -0.054 0.14 0.2 19 -0.23 193 212
neuron apoptosis 0.12 0.19 0.38 132 -10000 0 132
SHC 2-3/Grb2 -0.12 0.21 -10000 0 -0.41 132 132
SHC1 0.019 0.009 -10000 0 -10000 0 0
SHC2 -0.15 0.24 0.22 1 -0.49 141 142
SHC3 -0.092 0.18 0.22 1 -0.4 92 93
STAT3 (dimer) 0.026 0.012 0.22 1 -10000 0 1
NT3 (dimer)/TRKA -0.04 0.12 0.2 6 -0.22 149 155
RIN/GDP -0.043 0.1 0.24 4 -0.24 32 36
GIPC1 0.022 0.006 -10000 0 -10000 0 0
KRAS 0.023 0.014 0.33 1 -10000 0 1
DNAJA3 -0.098 0.15 0.22 2 -0.28 174 176
RIN/GTP 0.013 0.003 -10000 0 -10000 0 0
CCND1 0.012 0.021 0.32 2 -10000 0 2
MAGED1 0.021 0.023 -10000 0 -0.35 2 2
PTPN11 0.023 0.003 -10000 0 -10000 0 0
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) 0.031 0.055 0.28 22 -0.35 1 23
SHC/GRB2/SOS1 0.035 0.021 -10000 0 -10000 0 0
GRB2 0.022 0.006 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK -0.015 0.1 0.2 5 -0.21 105 110
TRKA/NEDD4-2 0.026 0.036 0.21 6 -0.24 5 11
ELMO1 0.019 0.033 -10000 0 -0.35 4 4
RhoG/GTP/ELMO1/DOCK1 0.024 0.035 -10000 0 -0.22 9 9
NGF -0.057 0.15 -10000 0 -0.35 112 112
HRAS 0.022 0.005 -10000 0 -10000 0 0
DOCK1 0.018 0.04 -10000 0 -0.35 6 6
GAB2 0.02 0.033 -10000 0 -0.35 4 4
RIT2 0.017 0.004 -10000 0 -10000 0 0
RIT1 0.018 0.01 -10000 0 -10000 0 0
FRS2 0.023 0.003 -10000 0 -10000 0 0
DNM1 0.018 0.04 -10000 0 -0.35 6 6
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.021 0.006 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP -0.086 0.16 0.18 1 -0.28 175 176
mol:GDP -0.067 0.14 0.29 4 -0.35 41 45
NGF (dimer) -0.057 0.15 -10000 0 -0.35 112 112
RhoG/GDP 0.015 0.023 -10000 0 -0.24 4 4
RIT1/GDP -0.048 0.085 0.22 2 -0.24 31 33
TIAM1 0.013 0.058 -10000 0 -0.35 13 13
PIK3R1 0.018 0.037 -10000 0 -0.35 5 5
BDNF (dimer)/TRKB 0.042 0.1 0.2 78 -0.21 49 127
KIDINS220/CRKL/C3G 0.031 0.01 -10000 0 -10000 0 0
SHC/RasGAP 0.024 0.03 -10000 0 -0.24 5 5
FRS2 family/SHP2 0.045 0.01 -10000 0 -10000 0 0
SHC/GRB2/SOS1/GAB1 0.041 0.032 -10000 0 -0.18 3 3
RIT1/GTP 0.013 0.007 -10000 0 -10000 0 0
NT3 (dimer) 0.003 0.091 0.28 5 -0.35 30 35
RAP1/GDP -0.041 0.083 -10000 0 -0.21 34 34
KIDINS220/CRKL 0.022 0.005 -10000 0 -10000 0 0
BDNF (dimer) 0.061 0.092 0.28 79 -10000 0 79
ubiquitin-dependent protein catabolic process -0.01 0.099 0.2 5 -0.21 98 103
Schwann cell development -0.035 0.029 -10000 0 -10000 0 0
EHD4 0.022 0.005 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 0.053 0.019 -10000 0 -10000 0 0
FRS2 family/SHP2/CRK family/C3G/GAB2 0.006 0.059 -10000 0 -0.23 20 20
RAP1B 0.023 0.002 -10000 0 -10000 0 0
RAP1A 0.023 0.001 -10000 0 -10000 0 0
CDC42/GTP -0.072 0.14 0.18 2 -0.2 249 251
ABL1 0.02 0.024 -10000 0 -0.35 2 2
SH2B family/GRB2/SOS1 0.031 0.01 -10000 0 -10000 0 0
Rap1/GTP 0.003 0.079 -10000 0 -0.28 15 15
STAT3 0.026 0.012 0.22 1 -10000 0 1
axon guidance -0.076 0.13 -10000 0 -0.19 249 249
MAPK3 -0.021 0.1 0.18 69 -0.19 98 167
MAPK1 -0.022 0.11 0.18 69 -0.19 100 169
CDC42/GDP -0.042 0.1 0.24 4 -0.24 32 36
NTF3 0.003 0.091 0.28 5 -0.35 30 35
NTF4 0.031 0.055 0.28 22 -0.35 1 23
NGF (dimer)/TRKA/FAIM -0.009 0.098 0.2 5 -0.21 96 101
PI3K 0.026 0.03 -10000 0 -0.24 5 5
FRS3 0.023 0.003 -10000 0 -10000 0 0
FAIM 0.022 0.017 -10000 0 -0.35 1 1
GAB1 0.019 0.033 -10000 0 -0.35 4 4
RASGRF1 -0.11 0.16 0.22 2 -0.3 179 181
SOS1 0.023 0.003 -10000 0 -10000 0 0
MCF2L -0.11 0.11 -10000 0 -0.22 234 234
RGS19 0.022 0.006 -10000 0 -10000 0 0
CDC42 0.022 0.004 -10000 0 -10000 0 0
RAS family/GTP -0.011 0.097 -10000 0 -0.38 11 11
Rac1/GDP -0.043 0.1 0.24 4 -0.24 34 38
NGF (dimer)/TRKA/GRIT -0.018 0.092 0.19 5 -0.2 99 104
neuron projection morphogenesis -0.12 0.24 -10000 0 -0.87 30 30
NGF (dimer)/TRKA/NEDD4-2 -0.01 0.099 0.2 5 -0.21 98 103
MAP2K1 0.027 0.088 0.18 116 -0.18 2 118
NGFR -0.097 0.17 0.28 1 -0.35 166 167
NGF (dimer)/TRKA/GIPC/GAIP -0.022 0.081 -10000 0 -0.2 86 86
RAS family/GTP/PI3K 0.013 0.027 0.17 1 -0.2 7 8
FRS2 family/SHP2/GRB2/SOS1 0.06 0.023 -10000 0 -10000 0 0
NRAS 0.023 0.001 -10000 0 -10000 0 0
GRB2/SOS1 0.031 0.01 -10000 0 -10000 0 0
PRKCI 0.021 0.007 -10000 0 -10000 0 0
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.022 0.005 -10000 0 -10000 0 0
PRKCZ 0.022 0.02 0.28 1 -0.35 1 2
MAPKKK cascade -0.13 0.25 -10000 0 -0.56 120 120
RASA1 0.019 0.037 -10000 0 -0.35 5 5
TRKA/c-Abl 0.025 0.038 0.21 6 -0.24 6 12
SQSTM1 0.022 0.004 -10000 0 -10000 0 0
BDNF (dimer)/TRKB/GIPC 0.051 0.095 0.21 77 -0.19 45 122
NGF (dimer)/TRKA/p62/Atypical PKCs 0.007 0.091 -10000 0 -0.18 87 87
MATK 0.014 0.055 0.28 1 -0.35 11 12
NEDD4L 0.021 0.017 -10000 0 -0.35 1 1
RAS family/GDP -0.052 0.061 -10000 0 -0.18 43 43
NGF (dimer)/TRKA -0.1 0.15 0.19 1 -0.29 181 182
Rac1/GTP -0.1 0.11 -10000 0 -0.23 189 189
FRS2 family/SHP2/CRK family 0.06 0.024 -10000 0 -10000 0 0
Ephrin B reverse signaling

Figure S27.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S27.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EFNB2 0.02 0.029 -10000 0 -0.35 3 3
EPHB2 0.025 0.02 0.28 3 -10000 0 3
EFNB1 -0.007 0.033 -10000 0 -0.28 6 6
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.023 0.078 0.29 1 -0.18 61 62
Ephrin B2/EPHB1-2 0.02 0.07 0.19 3 -0.18 53 56
neuron projection morphogenesis 0.011 0.069 0.22 1 -0.17 62 63
Ephrin B1/EPHB1-2/Tiam1 0.018 0.08 0.24 3 -0.18 64 67
DNM1 0.018 0.04 -10000 0 -0.35 6 6
cell-cell signaling 0.001 0.004 -10000 0 -10000 0 0
MAP2K4 -0.069 0.18 0.24 2 -0.48 76 78
YES1 -0.092 0.26 -10000 0 -0.7 77 77
Ephrin B1/EPHB1-2/NCK2 0.023 0.073 0.24 3 -0.18 54 57
PI3K -0.044 0.19 -10000 0 -0.49 73 73
mol:GDP 0.017 0.079 0.23 3 -0.18 64 67
ITGA2B 0.019 0.038 0.28 1 -0.35 5 6
endothelial cell proliferation 0.027 0.02 -10000 0 -0.2 3 3
FYN -0.091 0.26 -10000 0 -0.7 77 77
MAP3K7 -0.073 0.18 0.23 1 -0.51 76 77
FGR -0.091 0.25 -10000 0 -0.7 76 76
TIAM1 0.013 0.058 -10000 0 -0.35 13 13
PIK3R1 0.018 0.037 -10000 0 -0.35 5 5
RGS3 0.022 0.006 -10000 0 -10000 0 0
cell adhesion -0.075 0.19 0.25 1 -0.51 75 76
LYN -0.091 0.25 -10000 0 -0.69 77 77
Ephrin B1/EPHB1-2/Src Family Kinases -0.09 0.24 -10000 0 -0.64 79 79
Ephrin B1/EPHB1-2 -0.073 0.2 -10000 0 -0.56 73 73
SRC -0.09 0.25 -10000 0 -0.69 77 77
ITGB3 -0.038 0.14 0.28 2 -0.35 85 87
EPHB1 -0.013 0.11 -10000 0 -0.35 50 50
EPHB4 0.022 0.004 -10000 0 -10000 0 0
RAC1 0.022 0.005 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0.028 0.02 -10000 0 -0.2 3 3
alphaIIb/beta3 Integrin -0.015 0.11 0.21 3 -0.24 90 93
BLK -0.085 0.25 -10000 0 -0.69 76 76
HCK -0.088 0.25 -10000 0 -0.7 75 75
regulation of stress fiber formation -0.022 0.072 0.18 54 -0.23 3 57
MAPK8 -0.066 0.17 0.22 2 -0.47 75 77
Ephrin B1/EPHB1-2/RGS3 0.023 0.073 0.24 3 -0.18 54 57
endothelial cell migration -0.057 0.15 0.26 3 -0.43 70 73
NCK2 0.023 0.003 -10000 0 -10000 0 0
PTPN13 -0.036 0.16 -10000 0 -0.46 62 62
regulation of focal adhesion formation -0.022 0.072 0.18 54 -0.23 3 57
chemotaxis -0.021 0.072 0.18 54 -0.23 3 57
PIK3CA 0.02 0.018 -10000 0 -0.35 1 1
Rac1/GTP 0.018 0.074 0.26 1 -0.17 62 63
angiogenesis -0.073 0.2 -10000 0 -0.55 74 74
LCK -0.09 0.25 -10000 0 -0.69 77 77
Thromboxane A2 receptor signaling

Figure S28.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S28.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGM2 -0.012 0.11 -10000 0 -0.35 47 47
GNB1/GNG2 -0.044 0.074 -10000 0 -0.19 96 96
AKT1 -0.036 0.098 0.21 3 -0.23 41 44
EGF 0.031 0.052 0.28 20 -0.35 1 21
mol:TXA2 0 0.001 -10000 0 -10000 0 0
FGR -0.013 0.062 0.25 6 -0.26 2 8
mol:Ca2+ -0.065 0.14 0.24 3 -0.31 116 119
LYN -0.01 0.054 0.27 4 -10000 0 4
RhoA/GTP -0.027 0.057 -10000 0 -0.13 94 94
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.072 0.15 -10000 0 -0.34 101 101
GNG2 0.017 0.05 0.28 1 -0.35 9 10
ARRB2 0.021 0.006 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 -0.051 0.18 -10000 0 -0.55 51 51
G beta5/gamma2 -0.055 0.099 -10000 0 -0.25 94 94
PRKCH -0.076 0.16 -10000 0 -0.36 100 100
DNM1 0.018 0.04 -10000 0 -0.35 6 6
TXA2/TP beta/beta Arrestin3 0.011 0.026 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -10000 0 0
PTGDR -0.011 0.1 -10000 0 -0.35 45 45
G12 family/GTP -0.068 0.13 -10000 0 -0.3 109 109
ADRBK1 0.022 0.004 -10000 0 -10000 0 0
ADRBK2 0.021 0.017 -10000 0 -0.35 1 1
RhoA/GTP/ROCK1 0.029 0.008 -10000 0 -10000 0 0
mol:GDP 0.048 0.13 0.41 35 -10000 0 35
mol:NADP 0.022 0.02 0.28 1 -0.35 1 2
RAB11A 0.022 0.005 -10000 0 -10000 0 0
PRKG1 -0.13 0.18 -10000 0 -0.35 215 215
mol:IP3 -0.084 0.18 -10000 0 -0.38 116 116
cell morphogenesis 0.029 0.008 -10000 0 -10000 0 0
PLCB2 -0.12 0.24 -10000 0 -0.54 111 111
mol:cGMP 0 0.001 -10000 0 -10000 0 0
BLK -0.003 0.071 0.3 9 -0.2 1 10
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK -0.01 0.056 0.24 4 -0.22 1 5
RHOA 0.022 0.005 -10000 0 -10000 0 0
PTGIR 0.022 0.017 -10000 0 -0.35 1 1
PRKCB1 -0.081 0.17 -10000 0 -0.38 107 107
GNAQ 0.021 0.017 -10000 0 -0.35 1 1
mol:L-citrulline 0.022 0.02 0.28 1 -0.35 1 2
TXA2/TXA2-R family -0.11 0.23 -10000 0 -0.53 102 102
LCK -0.009 0.062 0.24 7 -0.22 1 8
TXA2/TP beta/beta Arrestin3/RAB11/GDP 0.012 0.055 -10000 0 -0.17 33 33
TXA2-R family/G12 family/GDP/G beta/gamma -0.002 0.094 -10000 0 -0.43 21 21
TXA2/TP beta/beta Arrestin2/RAB11/GDP 0.013 0.053 -10000 0 -0.17 30 30
MAPK14 -0.046 0.1 0.19 3 -0.23 91 94
TGM2/GTP -0.1 0.2 0.32 2 -0.44 123 125
MAPK11 -0.047 0.1 0.18 3 -0.23 95 98
ARHGEF1 -0.039 0.078 0.13 1 -0.18 98 99
GNAI2 0.022 0.005 -10000 0 -10000 0 0
JNK cascade -0.08 0.17 -10000 0 -0.38 103 103
RAB11/GDP 0.022 0.005 -10000 0 -10000 0 0
ICAM1 -0.054 0.12 -10000 0 -0.28 96 96
cAMP biosynthetic process -0.083 0.16 0.26 2 -0.36 123 125
Gq family/GTP/EBP50 -0.015 0.081 -10000 0 -0.21 64 64
actin cytoskeleton reorganization 0.029 0.008 -10000 0 -10000 0 0
SRC -0.011 0.058 0.25 5 -0.22 1 6
GNB5 0.022 0.005 -10000 0 -10000 0 0
GNB1 0.022 0.004 -10000 0 -10000 0 0
EGF/EGFR 0.012 0.074 0.25 20 -0.24 3 23
VCAM1 -0.062 0.14 -10000 0 -0.32 96 96
TP beta/Gq family/GDP/G beta5/gamma2 -0.051 0.18 -10000 0 -0.55 51 51
platelet activation -0.063 0.14 0.24 3 -0.3 101 104
PGI2/IP 0.016 0.012 -10000 0 -0.24 1 1
PRKACA -0.003 0.055 -10000 0 -0.19 39 39
Gq family/GDP/G beta5/gamma2 -0.042 0.16 -10000 0 -0.48 47 47
TXA2/TP beta/beta Arrestin2 -0.003 0.072 -10000 0 -0.37 16 16
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R -0.01 0.047 -10000 0 -0.18 35 35
mol:DAG -0.092 0.19 -10000 0 -0.43 107 107
EGFR 0.014 0.06 0.33 1 -0.35 13 14
TXA2/TP alpha -0.12 0.22 -10000 0 -0.49 122 122
Gq family/GTP -0.026 0.09 -10000 0 -0.23 74 74
YES1 -0.009 0.059 0.26 6 -10000 0 6
GNAI2/GTP -0.001 0.05 -10000 0 -0.16 34 34
PGD2/DP -0.006 0.072 -10000 0 -0.24 45 45
SLC9A3R1 0.023 0.02 0.28 3 -10000 0 3
FYN -0.012 0.058 0.26 5 -0.22 1 6
mol:NO 0.022 0.02 0.28 1 -0.35 1 2
GNA15 0.025 0.03 0.28 7 -10000 0 7
PGK/cGMP -0.068 0.11 -10000 0 -0.2 214 214
RhoA/GDP 0.022 0.005 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma 0.006 0.086 -10000 0 -0.28 14 14
NOS3 0.022 0.02 0.28 1 -0.35 1 2
RAC1 0.022 0.005 -10000 0 -10000 0 0
PRKCA -0.078 0.16 -10000 0 -0.37 102 102
PRKCB -0.081 0.16 -10000 0 -0.38 101 101
PRKCE -0.073 0.16 0.26 2 -0.36 95 97
PRKCD -0.079 0.17 -10000 0 -0.39 99 99
PRKCG -0.082 0.17 0.28 1 -0.39 104 105
muscle contraction -0.11 0.21 -10000 0 -0.49 103 103
PRKCZ -0.072 0.15 0.25 1 -0.34 101 102
ARR3 0.019 0.012 0.28 1 -10000 0 1
TXA2/TP beta 0.011 0.057 -10000 0 -0.17 34 34
PRKCQ -0.08 0.17 0.31 3 -0.38 105 108
MAPKKK cascade -0.1 0.21 -10000 0 -0.47 107 107
SELE -0.066 0.15 0.21 2 -0.34 96 98
TP beta/GNAI2/GDP/G beta/gamma 0.022 0.065 -10000 0 -0.24 3 3
ROCK1 0.023 0.004 -10000 0 -10000 0 0
GNA14 -0.01 0.1 -10000 0 -0.35 44 44
chemotaxis -0.12 0.25 -10000 0 -0.6 96 96
GNA12 0.022 0.005 -10000 0 -10000 0 0
GNA13 0.022 0.005 -10000 0 -10000 0 0
GNA11 0.015 0.049 -10000 0 -0.35 9 9
Rac1/GTP 0.016 0.004 -10000 0 -10000 0 0
Glypican 1 network

Figure S29.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S29.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GPC1/FGF2 dimer/FGFR1 dimer -0.079 0.12 -10000 0 -0.21 247 247
fibroblast growth factor receptor signaling pathway -0.079 0.12 -10000 0 -0.21 247 247
LAMA1 0.1 0.13 0.28 166 -0.35 4 170
PRNP -0.03 0.13 -10000 0 -0.35 73 73
GPC1/SLIT2 -0.002 0.091 -10000 0 -0.24 64 64
SMAD2 -0.016 0.033 0.18 6 -0.19 11 17
GPC1/PrPc/Cu2+ -0.003 0.081 -10000 0 -0.2 73 73
GPC1/Laminin alpha1 0.085 0.088 0.21 162 -0.24 4 166
TDGF1 0.013 0.092 0.28 17 -0.35 24 41
CRIPTO/GPC1 0.025 0.068 0.21 17 -0.24 24 41
APP/GPC1 0.033 0.007 -10000 0 -10000 0 0
mol:NO 0 0 -10000 0 -10000 0 0
YES1 -0.019 0.043 -10000 0 -0.21 23 23
FLT1 0.022 0.005 -10000 0 -10000 0 0
GPC1/TGFB/TGFBR1/TGFBR2 0.037 0.038 -10000 0 -0.21 11 11
SERPINC1 0.022 0.033 0.29 7 -10000 0 7
FYN -0.018 0.042 -10000 0 -0.21 22 22
FGR -0.023 0.051 -10000 0 -0.21 32 32
positive regulation of MAPKKK cascade 0.009 0.089 0.3 13 -0.28 20 33
SLIT2 -0.024 0.12 -10000 0 -0.35 64 64
GPC1/NRG 0.025 0.036 0.21 1 -0.24 8 9
NRG1 0.015 0.048 0.28 1 -0.35 8 9
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.043 0.013 -10000 0 -10000 0 0
LYN -0.017 0.041 -10000 0 -0.21 20 20
mol:Spermine -0.006 0.001 -10000 0 -10000 0 0
cell growth -0.079 0.12 -10000 0 -0.21 247 247
BMP signaling pathway -0.023 0.003 -10000 0 -10000 0 0
SRC -0.019 0.043 -10000 0 -0.21 23 23
TGFBR1 0.022 0.006 -10000 0 -10000 0 0
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.002 0.11 0.28 10 -0.35 39 49
GPC1 0.023 0.003 -10000 0 -10000 0 0
TGFBR1 (dimer) 0.022 0.006 -10000 0 -10000 0 0
VEGFA 0.023 0.003 -10000 0 -10000 0 0
BLK -0.006 0.059 0.15 35 -0.21 19 54
HCK -0.016 0.045 0.13 6 -0.21 22 28
FGF2 -0.17 0.18 -10000 0 -0.35 265 265
FGFR1 0.02 0.018 -10000 0 -0.35 1 1
VEGFR1 homodimer 0.022 0.005 -10000 0 -10000 0 0
TGFBR2 0.014 0.054 -10000 0 -0.35 11 11
cell death 0.033 0.007 -10000 0 -10000 0 0
ATIII/GPC1 0.03 0.025 0.22 7 -10000 0 7
PLA2G2A/GPC1 0.014 0.078 0.21 10 -0.24 39 49
LCK -0.018 0.044 0.14 3 -0.21 22 25
neuron differentiation 0.025 0.036 0.21 1 -0.24 8 9
PrPc/Cu2+ -0.02 0.089 -10000 0 -0.24 73 73
APP 0.023 0.004 -10000 0 -10000 0 0
TGFBR2 (dimer) 0.014 0.054 -10000 0 -0.35 11 11
LPA4-mediated signaling events

Figure S30.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S30.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ADCY4 -0.016 0.038 -10000 0 -0.2 20 20
ADCY5 -0.045 0.076 -10000 0 -0.2 96 96
ADCY6 -0.009 0.002 -10000 0 -10000 0 0
ADCY7 -0.008 0.003 -10000 0 -10000 0 0
ADCY1 -0.014 0.038 0.24 1 -0.2 18 19
ADCY2 -0.11 0.098 -10000 0 -0.2 267 267
ADCY3 -0.01 0.012 -10000 0 -0.2 2 2
ADCY8 -0.009 0.013 0.24 1 -10000 0 1
PRKCE -0.006 0.001 -10000 0 -10000 0 0
ADCY9 -0.035 0.066 -10000 0 -0.2 69 69
mol:DAG 0 0 -10000 0 -10000 0 0
cAMP biosynthetic process -0.051 0.094 0.22 20 -0.22 37 57
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

Figure S31.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S31.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
FOXP3 0.061 0.095 0.32 60 -10000 0 60
NFATC2 0 0.18 0.35 1 -0.47 37 38
NFATC3 0 0.091 -10000 0 -0.26 42 42
CD40LG -0.11 0.3 -10000 0 -0.78 67 67
ITCH 0.022 0.017 -10000 0 -10000 0 0
CBLB 0.022 0.017 -10000 0 -10000 0 0
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.046 0.26 0.44 13 -0.67 40 53
JUNB 0.018 0.037 -10000 0 -0.35 5 5
CaM/Ca2+/Calcineurin A alpha-beta B1 0.036 0.032 -10000 0 -10000 0 0
T cell anergy 0.019 0.052 0.27 8 -10000 0 8
TLE4 -0.029 0.18 -10000 0 -0.55 48 48
Jun/NFAT1-c-4/p21SNFT -0.043 0.31 -10000 0 -0.75 69 69
AP-1/NFAT1-c-4 -0.072 0.38 0.56 5 -0.88 65 70
IKZF1 -0.005 0.12 0.34 1 -0.35 30 31
T-helper 2 cell differentiation -0.066 0.22 -10000 0 -0.81 20 20
AP-1/NFAT1 -0.034 0.18 0.3 4 -0.34 71 75
CALM1 0.031 0.014 -10000 0 -10000 0 0
EGR2 -0.11 0.38 -10000 0 -1 58 58
EGR3 -0.14 0.42 -10000 0 -1.1 78 78
NFAT1/FOXP3 0.044 0.17 0.42 34 -0.34 32 66
EGR1 -0.022 0.12 -10000 0 -0.35 65 65
JUN 0.018 0.047 -10000 0 -0.35 7 7
EGR4 0.03 0.044 0.28 15 -10000 0 15
mol:Ca2+ 0.009 0.013 -10000 0 -10000 0 0
GBP3 -0.007 0.13 -10000 0 -0.39 30 30
FOSL1 0.042 0.069 0.28 40 -10000 0 40
NFAT1-c-4/MAF/IRF4 -0.067 0.33 0.46 2 -0.78 73 75
DGKA -0.002 0.11 -10000 0 -0.35 25 25
CREM 0.021 0.009 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.061 0.32 -10000 0 -0.77 75 75
CTLA4 0.022 0.13 0.3 50 -0.29 27 77
NFAT1-c-4 (dimer)/EGR1 -0.068 0.34 -10000 0 -0.8 77 77
NFAT1-c-4 (dimer)/EGR4 -0.041 0.33 0.5 1 -0.75 76 77
FOS -0.085 0.17 -10000 0 -0.35 152 152
IFNG -0.033 0.2 0.37 1 -0.68 23 24
T cell activation -0.071 0.2 -10000 0 -0.62 36 36
MAF -0.034 0.13 -10000 0 -0.35 75 75
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.069 0.28 0.7 72 -10000 0 72
TNF -0.074 0.3 0.38 2 -0.72 76 78
FASLG -0.15 0.46 -10000 0 -1.1 84 84
TBX21 0.026 0.059 0.35 3 -0.35 9 12
BATF3 0.02 0.014 0.28 1 -10000 0 1
PRKCQ -0.006 0.1 0.32 1 -0.35 42 43
PTPN1 -0.005 0.12 -10000 0 -0.34 30 30
NFAT1-c-4/ICER1 -0.053 0.32 -10000 0 -0.75 76 76
GATA3 0.025 0.058 0.28 13 -0.35 6 19
T-helper 1 cell differentiation -0.032 0.2 0.37 1 -0.66 23 24
IL2RA -0.043 0.26 0.44 16 -0.64 46 62
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.005 0.11 -10000 0 -0.35 28 28
E2F1 0.075 0.1 0.29 98 -10000 0 98
PPARG 0.004 0.084 0.33 1 -0.35 27 28
SLC3A2 -0.004 0.11 -10000 0 -0.35 27 27
IRF4 0.019 0.062 0.28 9 -0.35 10 19
PTGS2 -0.12 0.31 0.41 1 -0.78 69 70
CSF2 -0.11 0.3 -10000 0 -0.77 67 67
JunB/Fra1/NFAT1-c-4 -0.034 0.32 0.46 2 -0.74 71 73
IL4 -0.069 0.22 -10000 0 -0.86 20 20
IL5 -0.11 0.3 -10000 0 -0.77 67 67
IL2 -0.073 0.2 -10000 0 -0.63 36 36
IL3 -0.021 0.11 -10000 0 -0.66 12 12
RNF128 0.032 0.055 0.22 40 -10000 0 40
NFATC1 -0.07 0.28 -10000 0 -0.7 72 72
CDK4 0.065 0.19 0.56 46 -10000 0 46
PTPRK -0.004 0.12 0.34 1 -0.34 33 34
IL8 -0.073 0.32 0.42 4 -0.78 64 68
POU2F1 0.019 0.009 -10000 0 -10000 0 0
S1P4 pathway

Figure S32.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S32.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
GNAO1 -0.065 0.16 -10000 0 -0.35 120 120
CDC42/GTP -0.042 0.11 -10000 0 -0.2 134 134
PLCG1 -0.044 0.097 -10000 0 -0.2 126 126
mol:GTP 0 0 -10000 0 -10000 0 0
GNAI2 0.022 0.005 -10000 0 -10000 0 0
GNAI3 0.023 0.002 -10000 0 -10000 0 0
G12/G13 0.031 0.01 -10000 0 -10000 0 0
cell migration -0.042 0.1 -10000 0 -0.2 134 134
S1PR5 0.025 0.053 0.29 13 -0.35 4 17
S1PR4 0.02 0.026 0.28 1 -0.35 2 3
MAPK3 -0.045 0.099 -10000 0 -0.2 128 128
MAPK1 -0.041 0.097 -10000 0 -0.21 121 121
S1P/S1P5/Gi -0.037 0.1 0.17 2 -0.21 123 125
GNAI1 0.017 0.046 -10000 0 -0.35 8 8
CDC42/GDP 0.017 0.003 -10000 0 -10000 0 0
S1P/S1P5/G12 0.029 0.03 0.19 10 -0.2 3 13
RHOA -0.008 0.035 0.18 16 -0.17 2 18
S1P/S1P4/Gi -0.04 0.1 -10000 0 -0.21 127 127
mol:GDP 0 0 -10000 0 -10000 0 0
GNAZ 0.011 0.062 -10000 0 -0.35 15 15
S1P/S1P4/G12/G13 0.038 0.022 0.19 1 -0.18 2 3
GNA12 0.022 0.005 -10000 0 -10000 0 0
GNA13 0.022 0.005 -10000 0 -10000 0 0
CDC42 0.022 0.004 -10000 0 -10000 0 0
Noncanonical Wnt signaling pathway

Figure S33.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S33.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC2 -0.011 0.11 -10000 0 -0.35 46 46
GNB1/GNG2 -0.035 0.14 -10000 0 -0.38 37 37
mol:DAG -0.044 0.12 0.2 8 -0.36 35 43
PLCG1 -0.046 0.13 0.21 8 -0.37 35 43
YES1 -0.052 0.13 0.2 2 -0.42 30 32
FZD3 0.02 0.008 -10000 0 -10000 0 0
FZD6 0.02 0.018 -10000 0 -0.35 1 1
G protein -0.032 0.14 0.24 2 -0.39 33 35
MAP3K7 -0.12 0.13 0.2 4 -0.31 109 113
mol:Ca2+ -0.043 0.12 0.2 8 -0.35 35 43
mol:IP3 -0.044 0.12 0.2 8 -0.36 35 43
NLK -0.027 0.15 -10000 0 -0.81 19 19
GNB1 0.022 0.004 -10000 0 -10000 0 0
CAMK2A -0.12 0.14 0.23 4 -0.33 109 113
MAP3K7IP1 0 0 -10000 0 -10000 0 0
Noncanonical Wnts/FZD -0.047 0.14 -10000 0 -0.25 128 128
CSNK1A1 0.022 0.004 -10000 0 -10000 0 0
GNAS -0.051 0.13 0.21 3 -0.42 29 32
GO:0007205 -0.048 0.12 0.22 9 -0.36 36 45
WNT6 0.009 0.11 0.28 22 -0.35 34 56
WNT4 -0.066 0.16 -10000 0 -0.35 123 123
NFAT1/CK1 alpha -0.047 0.14 0.26 2 -0.37 42 44
GNG2 0.017 0.05 0.28 1 -0.35 9 10
WNT5A 0.011 0.064 -10000 0 -0.35 16 16
WNT11 0.035 0.098 0.28 46 -0.35 14 60
CDC42 -0.05 0.12 0.2 3 -0.4 29 32
Nephrin/Neph1 signaling in the kidney podocyte

Figure S34.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S34.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
positive regulation of NF-kappaB transcription factor activity -0.003 0.09 0.26 50 -0.22 11 61
KIRREL -0.017 0.11 -10000 0 -0.36 52 52
Nephrin/NEPH1Par3/Par6/Atypical PKCs 0.003 0.09 0.22 11 -0.26 50 61
PLCG1 0.022 0.005 -10000 0 -10000 0 0
ARRB2 0.021 0.006 -10000 0 -10000 0 0
WASL 0.022 0.005 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP 0.023 0.078 0.22 11 -0.19 49 60
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP -0.005 0.07 0.2 3 -0.21 48 51
FYN 0.017 0.12 0.23 97 -0.18 49 146
mol:Ca2+ 0.02 0.075 0.34 1 -0.19 48 49
mol:DAG 0.021 0.076 0.34 1 -0.19 48 49
NPHS2 -0.008 0.033 0.3 3 -10000 0 3
mol:IP3 0.021 0.076 0.34 1 -0.19 48 49
regulation of endocytosis 0.015 0.068 0.19 9 -0.17 49 58
Nephrin/NEPH1/podocin/Cholesterol 0.013 0.073 0.2 12 -0.19 50 62
establishment of cell polarity 0.003 0.09 0.22 11 -0.26 50 61
Nephrin/NEPH1/podocin/NCK1-2 0.029 0.08 0.31 2 -0.18 49 51
Nephrin/NEPH1/beta Arrestin2 0.016 0.069 0.2 9 -0.18 49 58
NPHS1 0.02 0.054 0.29 13 -10000 0 13
Nephrin/NEPH1/podocin 0.014 0.072 0.2 12 -0.18 49 61
TJP1 0.022 0.005 -10000 0 -10000 0 0
NCK1 0.021 0.023 -10000 0 -0.35 2 2
NCK2 0.023 0.003 -10000 0 -10000 0 0
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 0.021 0.076 0.35 1 -0.19 48 49
CD2AP 0.022 0.004 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/GRB2 0.02 0.076 0.24 4 -0.19 49 53
GRB2 0.022 0.006 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 0.007 0.13 0.23 91 -0.2 64 155
cytoskeleton organization -0.016 0.079 0.22 19 -0.22 47 66
Nephrin/NEPH1 0.007 0.064 0.18 11 -0.17 50 61
Nephrin/NEPH1/ZO-1 0.014 0.077 0.2 11 -0.2 50 61
BMP receptor signaling

Figure S35.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S35.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BMP7/BMPR2/BMPR1A-1B/FS 0.018 0.11 0.23 17 -0.19 93 110
SMAD6-7/SMURF1 0.041 0.024 -10000 0 -0.21 3 3
NOG 0.042 0.072 0.28 42 -0.35 1 43
SMAD9 -0.071 0.19 -10000 0 -0.49 83 83
SMAD4 0.022 0.005 -10000 0 -10000 0 0
SMAD5 -0.026 0.097 -10000 0 -0.34 23 23
BMP7/USAG1 0.021 0.11 0.22 53 -0.25 55 108
SMAD5/SKI -0.022 0.11 -10000 0 -0.35 28 28
SMAD1 0.004 0.064 0.25 2 -0.42 6 8
BMP2 -0.009 0.1 -10000 0 -0.35 44 44
SMAD1/SMAD1/SMAD4 0.015 0.06 -10000 0 -0.32 6 6
BMPR1A 0.022 0.005 -10000 0 -10000 0 0
BMPR1B 0.001 0.088 0.28 1 -0.35 30 31
BMPR1A-1B/BAMBI 0.024 0.075 0.21 7 -0.22 39 46
AHSG 0.024 0.036 0.28 10 -10000 0 10
CER1 0.018 0.005 -10000 0 -10000 0 0
BMP2-4/CER1 0.015 0.086 0.2 8 -0.22 55 63
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.045 0.11 -10000 0 -0.34 38 38
BMP2-4 (homodimer) 0.002 0.099 0.21 8 -0.26 59 67
RGMB 0.022 0.017 -10000 0 -0.35 1 1
BMP6/BMPR2/BMPR1A-1B 0.035 0.067 0.21 1 -0.2 36 37
RGMA -0.057 0.15 -10000 0 -0.35 111 111
SMURF1 0.022 0.004 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.042 0.1 -10000 0 -0.31 42 42
BMP2-4/USAG1 0.012 0.12 0.2 41 -0.23 82 123
SMAD6/SMURF1/SMAD5 -0.024 0.11 -10000 0 -0.36 27 27
SOSTDC1 0.018 0.12 0.28 38 -0.35 31 69
BMP7/BMPR2/BMPR1A-1B 0.035 0.083 0.21 21 -0.2 47 68
SKI 0.022 0.004 -10000 0 -10000 0 0
BMP6 (homodimer) 0.015 0.054 -10000 0 -0.35 11 11
HFE2 0.016 0.018 0.28 2 -10000 0 2
ZFYVE16 0.022 0.005 -10000 0 -10000 0 0
MAP3K7 0.023 0.003 -10000 0 -10000 0 0
BMP2-4/CHRD -0.016 0.12 0.2 8 -0.23 110 118
SMAD5/SMAD5/SMAD4 -0.022 0.11 -10000 0 -0.36 26 26
MAPK1 0.022 0.005 -10000 0 -10000 0 0
TAK1/TAB family -0.025 0.11 -10000 0 -0.28 42 42
BMP7 (homodimer) 0.017 0.11 0.29 29 -0.35 28 57
NUP214 0.021 0.006 -10000 0 -10000 0 0
BMP6/FETUA 0.026 0.048 0.21 10 -0.25 11 21
SMAD1/SKI 0.012 0.071 0.24 2 -0.39 7 9
SMAD6 0.021 0.017 -10000 0 -0.35 1 1
CTDSP2 0.023 0.001 -10000 0 -10000 0 0
BMP2-4/FETUA 0.021 0.082 0.2 15 -0.22 47 62
MAP3K7IP1 0 0 -10000 0 -10000 0 0
GREM1 -0.069 0.16 -10000 0 -0.35 126 126
BMPR2 (homodimer) 0.023 0.003 -10000 0 -10000 0 0
GADD34/PP1CA 0.043 0.014 -10000 0 -10000 0 0
BMPR1A-1B (homodimer) 0.016 0.064 0.21 1 -0.24 28 29
CHRDL1 -0.23 0.17 -10000 0 -0.35 352 352
ENDOFIN/SMAD1 0.011 0.071 0.24 2 -0.38 7 9
SMAD6-7/SMURF1/SMAD1 0.028 0.075 -10000 0 -0.37 7 7
SMAD6/SMURF1 0.022 0.004 -10000 0 -10000 0 0
BAMBI 0.015 0.073 0.28 8 -0.35 16 24
SMURF2 0.022 0.005 -10000 0 -10000 0 0
BMP2-4/CHRDL1 -0.15 0.14 0.2 2 -0.23 359 361
BMP2-4/GREM1 -0.042 0.14 0.2 7 -0.24 161 168
SMAD7 0.021 0.023 -10000 0 -0.35 2 2
SMAD8A/SMAD8A/SMAD4 -0.067 0.19 -10000 0 -0.46 89 89
SMAD1/SMAD6 0.01 0.073 0.24 2 -0.39 7 9
TAK1/SMAD6 0.033 0.007 -10000 0 -10000 0 0
BMP7 0.017 0.11 0.29 29 -0.35 28 57
BMP6 0.015 0.054 -10000 0 -0.35 11 11
MAP3K7IP2 0 0 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.037 0.11 -10000 0 -0.3 50 50
PPM1A 0.022 0.004 -10000 0 -10000 0 0
SMAD1/SMURF2 0.013 0.069 0.24 2 -0.39 7 9
SMAD7/SMURF1 0.031 0.019 -10000 0 -0.24 2 2
CTDSPL 0.022 0.004 -10000 0 -10000 0 0
PPP1CA 0.022 0.004 -10000 0 -10000 0 0
XIAP 0.023 0.002 -10000 0 -10000 0 0
CTDSP1 0.023 0.003 -10000 0 -10000 0 0
PPP1R15A 0.023 0.004 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.064 0.14 -10000 0 -0.38 62 62
CHRD -0.037 0.13 -10000 0 -0.35 80 80
BMPR2 0.023 0.003 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.049 0.11 -10000 0 -0.34 40 40
BMP4 0.01 0.084 0.28 9 -0.35 23 32
FST -0.016 0.12 0.28 6 -0.35 57 63
BMP2-4/NOG 0.025 0.1 0.22 41 -0.22 60 101
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 0.041 0.082 0.23 2 -0.19 47 49
Plasma membrane estrogen receptor signaling

Figure S36.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S36.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 0.024 0.074 0.19 1 -0.18 60 61
ER alpha/Gai/GDP/Gbeta gamma -0.11 0.22 -10000 0 -0.47 92 92
AKT1 -0.082 0.25 -10000 0 -0.72 68 68
PIK3CA 0.02 0.018 -10000 0 -0.35 1 1
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.081 0.26 -10000 0 -0.73 68 68
mol:Ca2+ -0.033 0.11 0.17 3 -0.35 49 52
IGF1R 0.008 0.07 -10000 0 -0.35 19 19
E2/ER alpha (dimer)/Striatin 0.004 0.073 -10000 0 -0.2 56 56
SHC1 0.019 0.009 -10000 0 -10000 0 0
apoptosis 0.078 0.24 0.68 68 -10000 0 68
RhoA/GTP 0.002 0.053 -10000 0 -0.16 46 46
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.076 0.18 -10000 0 -0.41 81 81
regulation of stress fiber formation 0.021 0.066 0.26 2 -0.22 13 15
E2/ERA-ERB (dimer) 0.005 0.072 0.19 1 -0.2 54 55
KRAS 0.023 0.014 0.33 1 -10000 0 1
G13/GTP 0.005 0.064 -10000 0 -0.18 53 53
pseudopodium formation -0.021 0.066 0.22 13 -0.26 2 15
E2/ER alpha (dimer)/PELP1 0.004 0.07 -10000 0 -0.2 52 52
GRB2 0.022 0.006 -10000 0 -10000 0 0
GNG2 0.017 0.05 0.28 1 -0.35 9 10
GNAO1 -0.065 0.16 -10000 0 -0.35 120 120
HRAS 0.022 0.005 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.085 0.2 0.21 1 -0.5 76 77
E2/ER beta (dimer) 0.017 0.008 0.19 1 -10000 0 1
mol:GDP -0.019 0.097 -10000 0 -0.28 57 57
mol:NADP -0.085 0.2 0.21 1 -0.5 76 77
PIK3R1 0.018 0.037 -10000 0 -0.35 5 5
mol:IP3 -0.035 0.11 -10000 0 -0.36 49 49
IGF-1R heterotetramer 0.008 0.07 -10000 0 -0.35 19 19
PLCB1 -0.033 0.12 -10000 0 -0.37 52 52
PLCB2 -0.03 0.12 -10000 0 -0.36 49 49
IGF1 -0.048 0.15 -10000 0 -0.35 99 99
mol:L-citrulline -0.085 0.2 0.21 1 -0.5 76 77
RHOA 0.022 0.005 -10000 0 -10000 0 0
Gai/GDP -0.19 0.31 -10000 0 -0.62 174 174
JNK cascade 0.017 0.008 0.19 1 -10000 0 1
BCAR1 0.02 0.007 -10000 0 -10000 0 0
ESR2 0.023 0.012 0.28 1 -10000 0 1
GNAQ 0.021 0.017 -10000 0 -0.35 1 1
ESR1 -0.017 0.11 -10000 0 -0.35 54 54
Gq family/GDP/Gbeta gamma -0.065 0.23 -10000 0 -0.66 57 57
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 -0.02 0.12 -10000 0 -0.63 13 13
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.072 0.17 -10000 0 -0.43 68 68
GNAZ 0.011 0.062 -10000 0 -0.35 15 15
E2/ER alpha (dimer) -0.011 0.078 -10000 0 -0.24 54 54
STRN 0.021 0.023 -10000 0 -0.35 2 2
GNAL -0.031 0.13 -10000 0 -0.35 74 74
PELP1 0.021 0.006 -10000 0 -10000 0 0
MAPK11 0.008 0.014 -10000 0 -0.2 2 2
GNAI2 0.022 0.005 -10000 0 -10000 0 0
GNAI3 0.023 0.002 -10000 0 -10000 0 0
GNAI1 0.017 0.046 -10000 0 -0.35 8 8
HBEGF -0.092 0.2 0.28 3 -0.45 81 84
cAMP biosynthetic process -0.019 0.087 0.12 1 -0.18 108 109
SRC -0.11 0.2 0.21 4 -0.46 84 88
PI3K 0.026 0.03 -10000 0 -0.24 5 5
GNB1 0.022 0.004 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma 0.004 0.097 -10000 0 -0.28 46 46
SOS1 0.023 0.003 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.091 0.16 -10000 0 -0.37 92 92
Gs family/GTP -0.015 0.09 0.15 1 -0.18 108 109
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.041 0.015 0.22 1 -10000 0 1
vasodilation -0.081 0.19 0.2 1 -0.47 76 77
mol:DAG -0.035 0.11 -10000 0 -0.36 49 49
Gs family/GDP/Gbeta gamma -0.032 0.11 -10000 0 -0.3 52 52
MSN -0.022 0.069 0.24 11 -0.28 2 13
Gq family/GTP -0.027 0.12 -10000 0 -0.39 48 48
mol:PI-3-4-5-P3 -0.077 0.25 -10000 0 -0.7 68 68
NRAS 0.023 0.001 -10000 0 -10000 0 0
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.081 0.19 0.47 76 -0.2 1 77
GRB2/SOS1 0.031 0.01 -10000 0 -10000 0 0
RhoA/GDP -0.007 0.097 -10000 0 -0.3 47 47
NOS3 -0.09 0.21 -10000 0 -0.52 76 76
GNA11 0.015 0.049 -10000 0 -0.35 9 9
MAPKKK cascade -0.07 0.2 -10000 0 -0.53 74 74
E2/ER alpha (dimer)/PELP1/Src -0.082 0.18 0.25 1 -0.43 81 82
ruffle organization -0.021 0.066 0.22 13 -0.26 2 15
ROCK2 -0.018 0.076 0.26 12 -0.3 2 14
GNA14 -0.01 0.1 -10000 0 -0.35 44 44
GNA15 0.025 0.03 0.28 7 -10000 0 7
GNA13 0.022 0.005 -10000 0 -10000 0 0
MMP9 -0.091 0.19 0.3 6 -0.45 77 83
MMP2 -0.1 0.19 0.25 2 -0.45 84 86
amb2 Integrin signaling

Figure S37.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S37.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
alphaM/beta2 Integrin/proMMP-2 0.032 0.06 0.21 5 -0.21 22 27
alphaM/beta2 Integrin/GPIbA 0.042 0.043 0.26 6 -0.21 4 10
alphaM/beta2 Integrin/proMMP-9 0.11 0.094 0.22 201 -0.2 2 203
PLAUR 0.023 0.016 0.28 2 -10000 0 2
HMGB1 0.022 0.015 -10000 0 -10000 0 0
alphaM/beta2 Integrin/Talin 0.044 0.038 0.24 6 -0.2 3 9
AGER 0.022 0.022 -10000 0 -0.35 1 1
RAP1A 0.023 0.001 -10000 0 -10000 0 0
SELPLG 0.024 0.016 0.28 2 -10000 0 2
mol:LDL 0 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 0.06 0.065 0.25 8 -0.19 20 28
mol:GTP 0 0 -10000 0 -10000 0 0
MMP9 0.13 0.13 0.28 213 -10000 0 213
CYR61 -0.009 0.1 -10000 0 -0.35 44 44
TLN1 0.022 0.005 -10000 0 -10000 0 0
Rap1/GTP -0.003 0.1 0.21 1 -0.29 31 32
RHOA 0.022 0.005 -10000 0 -10000 0 0
P-selectin oligomer -0.097 0.17 -10000 0 -0.35 162 162
MYH2 -0.017 0.12 0.22 11 -0.41 23 34
MST1R 0.046 0.078 0.28 50 -0.35 1 51
leukocyte activation during inflammatory response 0.047 0.055 0.19 30 -0.17 9 39
APOB 0.016 0.044 0.3 2 -0.35 6 8
mol:GDP 0 0 -10000 0 -10000 0 0
complement component iC3b receptor activity 0 0 -10000 0 -10000 0 0
MMP2 0.006 0.072 -10000 0 -0.35 20 20
JAM3 -0.073 0.16 -10000 0 -0.35 133 133
GP1BA 0.02 0.021 0.28 1 -0.35 1 2
alphaM/beta2 Integrin/CTGF 0.038 0.052 0.24 5 -0.2 15 20
alphaM/beta2 Integrin -0.008 0.098 0.21 8 -0.31 25 33
JAM3 homodimer -0.073 0.16 -10000 0 -0.35 133 133
ICAM2 0.022 0.005 -10000 0 -10000 0 0
ICAM1 0.024 0.026 0.3 4 -10000 0 4
phagocytosis triggered by activation of immune response cell surface activating receptor -0.007 0.1 0.22 7 -0.32 25 32
cell adhesion 0.041 0.043 0.26 6 -0.2 4 10
NFKB1 0.024 0.09 0.32 10 -0.32 16 26
THY1 0.022 0.005 -10000 0 -10000 0 0
RhoA/GDP 0.016 0.004 -10000 0 -10000 0 0
Lipoprotein(a) 0.033 0.047 0.19 30 -0.2 6 36
alphaM/beta2 Integrin/LRP/tPA 0.028 0.078 0.21 5 -0.19 48 53
IL6 -0.005 0.12 0.31 10 -0.58 16 26
ITGB2 0.025 0.029 0.28 5 -10000 0 5
elevation of cytosolic calcium ion concentration 0.053 0.041 0.22 11 -0.19 2 13
alphaM/beta2 Integrin/JAM2/JAM3 -0.075 0.16 0.28 2 -0.25 224 226
JAM2 -0.1 0.18 -10000 0 -0.35 176 176
alphaM/beta2 Integrin/ICAM1 0.074 0.065 0.27 11 -0.17 3 14
alphaM/beta2 Integrin/uPA/Plg 0.04 0.075 0.23 16 -0.18 36 52
RhoA/GTP -0.022 0.13 0.24 7 -0.33 49 56
positive regulation of phagocytosis 0.007 0.083 0.25 7 -0.23 21 28
Ron/MSP 0.05 0.056 0.21 54 -0.24 1 55
alphaM/beta2 Integrin/uPAR/uPA 0.055 0.042 0.23 11 -0.19 2 13
alphaM/beta2 Integrin/uPAR 0.045 0.04 0.23 8 -0.2 3 11
PLAU 0.023 0.02 0.28 3 -10000 0 3
PLAT -0.014 0.11 -10000 0 -0.35 48 48
actin filament polymerization -0.018 0.12 0.23 11 -0.39 25 36
MST1 0.025 0.026 0.28 5 -10000 0 5
alphaM/beta2 Integrin/lipoprotein(a) 0.052 0.058 0.21 30 -0.18 9 39
TNF 0.008 0.1 0.35 10 -0.34 15 25
RAP1B 0.023 0.002 -10000 0 -10000 0 0
alphaM/beta2 Integrin/uPA 0.045 0.039 0.23 9 -0.2 2 11
fibrinolysis 0.038 0.074 0.22 16 -0.18 36 52
HCK 0.025 0.03 0.28 7 -10000 0 7
dendritic cell antigen processing and presentation -0.007 0.1 0.22 7 -0.32 25 32
VTN -0.023 0.12 0.3 3 -0.35 63 66
alphaM/beta2 Integrin/CYR61 0.024 0.078 0.21 5 -0.21 45 50
LPA 0.036 0.061 0.28 30 -10000 0 30
LRP1 0.022 0.023 -10000 0 -0.35 2 2
cell migration 0.052 0.065 0.24 9 -0.18 18 27
FN1 0.019 0.036 -10000 0 -0.35 5 5
alphaM/beta2 Integrin/Thy1 0.044 0.038 0.24 6 -0.2 3 9
MPO 0.025 0.03 0.28 7 -10000 0 7
KNG1 0.031 0.058 0.29 24 -10000 0 24
RAP1/GDP 0.031 0.003 -10000 0 -10000 0 0
ROCK1 -0.022 0.13 0.22 11 -0.38 33 44
ELA2 0 0 -10000 0 -10000 0 0
PLG -0.004 0.11 0.28 8 -0.35 41 49
CTGF 0.014 0.056 -10000 0 -0.35 12 12
alphaM/beta2 Integrin/Hck 0.045 0.045 0.26 10 -0.2 2 12
ITGAM 0.021 0.036 0.28 2 -0.35 3 5
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.023 0.11 0.3 5 -0.19 154 159
HP 0.046 0.15 0.28 104 -0.35 35 139
leukocyte adhesion -0.063 0.14 0.28 2 -0.29 94 96
SELP -0.097 0.17 -10000 0 -0.35 162 162
S1P5 pathway

Figure S38.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S38.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.036 0.1 0.19 125 -10000 0 125
GNAI2 0.022 0.005 -10000 0 -10000 0 0
S1P/S1P5/G12 0.029 0.03 0.19 10 -0.2 3 13
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 -0.065 0.16 -10000 0 -0.35 120 120
RhoA/GTP -0.036 0.1 -10000 0 -0.2 125 125
negative regulation of cAMP metabolic process -0.036 0.1 0.17 2 -0.21 123 125
GNAZ 0.011 0.062 -10000 0 -0.35 15 15
GNAI3 0.023 0.002 -10000 0 -10000 0 0
GNA12 0.022 0.005 -10000 0 -10000 0 0
S1PR5 0.025 0.053 0.29 13 -0.35 4 17
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi -0.037 0.1 0.17 2 -0.21 123 125
RhoA/GDP 0.016 0.004 -10000 0 -10000 0 0
RHOA 0.022 0.005 -10000 0 -10000 0 0
GNAI1 0.017 0.046 -10000 0 -0.35 8 8
Syndecan-1-mediated signaling events

Figure S39.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S39.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.022 0.017 -10000 0 -0.35 1 1
CCL5 0.021 0.046 0.28 6 -0.35 5 11
SDCBP 0.021 0.007 -10000 0 -10000 0 0
FGFR/FGF2/Syndecan-1 0.071 0.09 0.25 33 -0.29 2 35
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
RP11-540L11.1 0 0 -10000 0 -10000 0 0
Syndecan-1/Laminin-5 0.065 0.089 0.26 14 -0.28 4 18
Syndecan-1/Syntenin 0.066 0.088 0.25 17 -0.28 4 21
MAPK3 0.053 0.081 0.21 21 -0.26 4 25
HGF/MET -0.02 0.11 0.21 4 -0.25 99 103
TGFB1/TGF beta receptor Type II 0.022 0.017 -10000 0 -0.35 1 1
BSG 0.021 0.006 -10000 0 -10000 0 0
keratinocyte migration 0.064 0.088 0.26 14 -0.27 4 18
Syndecan-1/RANTES 0.07 0.092 0.25 24 -0.31 5 29
Syndecan-1/CD147 0.072 0.09 0.26 12 -0.27 4 16
Syndecan-1/Syntenin/PIP2 0.062 0.084 0.23 17 -0.27 4 21
LAMA5 0.022 0.015 0.33 1 -10000 0 1
positive regulation of cell-cell adhesion 0.059 0.081 0.22 16 -0.26 4 20
MMP7 0.027 0.13 0.28 59 -0.35 34 93
HGF -0.048 0.14 -10000 0 -0.35 98 98
Syndecan-1/CASK 0.055 0.086 0.21 32 -0.26 6 38
Syndecan-1/HGF/MET 0.045 0.12 0.27 16 -0.3 25 41
regulation of cell adhesion 0.045 0.074 0.24 9 -0.28 2 11
HPSE 0.017 0.051 0.28 2 -0.35 9 11
positive regulation of cell migration 0.071 0.09 0.25 33 -0.29 2 35
SDC1 0.072 0.087 0.24 32 -0.3 2 34
Syndecan-1/Collagen 0.071 0.09 0.25 33 -0.29 2 35
PPIB 0.023 0.012 0.28 1 -10000 0 1
MET 0.021 0.04 0.28 4 -0.35 4 8
PRKACA 0.022 0.005 -10000 0 -10000 0 0
MMP9 0.13 0.13 0.28 213 -10000 0 213
MAPK1 0.054 0.077 0.2 18 -0.25 4 22
homophilic cell adhesion 0.07 0.093 0.25 34 -0.27 3 37
MMP1 0.16 0.13 0.28 274 -10000 0 274
LPA receptor mediated events

Figure S40.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S40.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 0.026 0.068 0.19 1 -0.22 32 33
NF kappa B1 p50/RelA/I kappa B alpha 0.004 0.089 0.31 4 -0.27 7 11
AP1 -0.033 0.12 -10000 0 -0.19 174 174
mol:PIP3 -0.024 0.063 -10000 0 -0.19 52 52
AKT1 -0.01 0.07 0.26 7 -0.28 10 17
PTK2B -0.024 0.096 0.19 1 -0.26 54 55
RHOA -0.001 0.057 0.19 5 -0.29 12 17
PIK3CB 0.022 0.005 -10000 0 -10000 0 0
mol:Ca2+ -0.01 0.062 0.22 9 -0.26 5 14
MAGI3 0.023 0.002 -10000 0 -10000 0 0
RELA 0.022 0.004 -10000 0 -10000 0 0
apoptosis -0.008 0.071 -10000 0 -0.21 50 50
HRAS/GDP 0.016 0.004 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization -0.027 0.092 0.21 8 -0.28 36 44
NF kappa B1 p50/RelA 0.008 0.092 0.2 3 -0.23 35 38
endothelial cell migration -0.009 0.095 -10000 0 -0.38 28 28
ADCY4 -0.054 0.12 -10000 0 -0.34 56 56
ADCY5 -0.08 0.14 -10000 0 -0.35 77 77
ADCY6 -0.047 0.11 -10000 0 -0.32 48 48
ADCY7 -0.044 0.11 -10000 0 -0.34 41 41
ADCY1 -0.053 0.12 -10000 0 -0.34 53 53
ADCY2 -0.13 0.16 -10000 0 -0.38 123 123
ADCY3 -0.048 0.11 -10000 0 -0.32 52 52
ADCY8 -0.044 0.11 -10000 0 -0.32 43 43
ADCY9 -0.072 0.14 -10000 0 -0.35 82 82
GSK3B -0.024 0.095 0.23 8 -0.27 44 52
arachidonic acid secretion -0.064 0.13 -10000 0 -0.33 65 65
GNG2 0.017 0.05 0.28 1 -0.35 9 10
TRIP6 0.011 0.035 0.15 1 -0.33 5 6
GNAO1 -0.047 0.11 -10000 0 -0.23 127 127
HRAS 0.022 0.005 -10000 0 -10000 0 0
NFKBIA -0.017 0.087 0.26 6 -0.24 29 35
GAB1 0.019 0.033 -10000 0 -0.35 4 4
mol:GTP 0 0 -10000 0 -10000 0 0
lamellipodium assembly 0.002 0.18 -10000 0 -0.83 23 23
JUN 0.018 0.043 -10000 0 -0.35 7 7
LPA/LPA2/NHERF2 0.027 0.024 0.19 2 -10000 0 2
TIAM1 -0.014 0.21 -10000 0 -0.96 23 23
PIK3R1 0.018 0.037 -10000 0 -0.35 5 5
mol:IP3 -0.01 0.061 0.22 9 -0.19 22 31
PLCB3 0.012 0.035 0.18 16 -10000 0 16
FOS -0.086 0.17 -10000 0 -0.35 152 152
positive regulation of mitosis -0.064 0.13 -10000 0 -0.33 65 65
LPA/LPA1-2-3 0.027 0.085 0.2 23 -0.2 49 72
mol:Ca ++ 0 0 -10000 0 -10000 0 0
JNK cascade 0 0 -10000 0 -10000 0 0
BCAR1 0.02 0.007 -10000 0 -10000 0 0
stress fiber formation -0.01 0.082 0.21 1 -0.3 18 19
GNAZ -0.006 0.067 -10000 0 -0.22 40 40
EGFR/PI3K-beta/Gab1 0 0.073 -10000 0 -0.2 52 52
positive regulation of dendritic cell cytokine production 0.026 0.083 0.19 23 -0.2 49 72
LPA/LPA2/MAGI-3 0.028 0.024 0.19 2 -10000 0 2
ARHGEF1 -0.007 0.056 0.18 18 -0.2 23 41
GNAI2 -0.001 0.056 -10000 0 -0.23 27 27
GNAI3 -0.001 0.057 -10000 0 -0.23 28 28
GNAI1 -0.003 0.061 -10000 0 -0.23 33 33
LPA/LPA3 0.01 0.07 0.19 23 -0.19 38 61
LPA/LPA2 0.015 0.024 0.19 2 -0.095 13 15
LPA/LPA1 0.004 0.068 -10000 0 -0.25 32 32
HB-EGF/EGFR 0.047 0.055 0.22 5 -0.2 12 17
HBEGF 0.042 0.066 0.11 210 -10000 0 210
mol:DAG -0.01 0.061 0.22 9 -0.19 22 31
cAMP biosynthetic process -0.083 0.13 0.21 2 -0.27 125 127
NFKB1 0.022 0.017 -10000 0 -0.35 1 1
SRC 0.022 0.005 -10000 0 -10000 0 0
GNB1 0.022 0.004 -10000 0 -10000 0 0
LYN -0.008 0.089 0.27 10 -0.24 29 39
GNAQ 0.001 0.051 -10000 0 -0.2 26 26
LPAR2 0.024 0.021 0.3 3 -10000 0 3
LPAR3 0.017 0.098 0.28 24 -0.35 25 49
LPAR1 0.008 0.069 -10000 0 -0.26 26 26
IL8 0.033 0.14 0.3 13 -0.35 22 35
PTK2 -0.015 0.06 0.18 7 -0.19 42 49
Rac1/GDP 0.016 0.003 -10000 0 -10000 0 0
CASP3 -0.008 0.071 -10000 0 -0.21 50 50
EGFR 0.014 0.06 0.33 1 -0.35 13 14
PLCG1 -0.007 0.062 0.16 6 -0.21 32 38
PLD2 -0.017 0.064 0.18 7 -0.2 48 55
G12/G13 0.029 0.06 -10000 0 -0.21 25 25
PI3K-beta 0 0.065 -10000 0 -0.28 14 14
cell migration 0.001 0.065 -10000 0 -0.26 22 22
SLC9A3R2 0.022 0.005 -10000 0 -10000 0 0
PXN -0.01 0.083 0.21 1 -0.3 18 19
HRAS/GTP -0.064 0.13 -10000 0 -0.25 136 136
RAC1 0.022 0.005 -10000 0 -10000 0 0
MMP9 0.13 0.13 0.28 213 -10000 0 213
PRKCE 0.023 0.004 -10000 0 -10000 0 0
PRKCD -0.015 0.068 0.21 12 -0.25 7 19
Gi(beta/gamma) -0.046 0.11 -10000 0 -0.32 50 50
mol:LPA -0.004 0.026 -10000 0 -0.14 16 16
TRIP6/p130 Cas/FAK1/Paxillin 0.006 0.081 -10000 0 -0.34 11 11
MAPKKK cascade -0.064 0.13 -10000 0 -0.33 65 65
contractile ring contraction involved in cytokinesis -0.002 0.059 0.19 5 -0.27 14 19
mol:GDP 0 0 -10000 0 -10000 0 0
GNA14 -0.015 0.078 -10000 0 -0.22 65 65
GNA15 0.003 0.051 0.12 3 -0.2 25 28
GNA12 0.022 0.005 -10000 0 -10000 0 0
GNA13 0.022 0.005 -10000 0 -10000 0 0
MAPT -0.028 0.094 0.22 8 -0.28 36 44
GNA11 -0.002 0.056 -10000 0 -0.2 34 34
Rac1/GTP 0.001 0.19 -10000 0 -0.88 23 23
MMP2 -0.009 0.095 -10000 0 -0.39 28 28
Signaling events mediated by Stem cell factor receptor (c-Kit)

Figure S41.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S41.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K1 -0.049 0.13 -10000 0 -0.4 47 47
CRKL -0.053 0.14 -10000 0 -0.43 49 49
HRAS -0.036 0.12 -10000 0 -0.37 41 41
mol:PIP3 -0.022 0.15 0.26 4 -0.4 41 45
SPRED1 0.022 0.005 -10000 0 -10000 0 0
SPRED2 0.022 0.017 -10000 0 -0.35 1 1
GAB1 -0.055 0.15 -10000 0 -0.43 53 53
FOXO3 -0.036 0.14 0.34 2 -0.4 43 45
AKT1 -0.037 0.15 -10000 0 -0.43 46 46
BAD -0.034 0.14 -10000 0 -0.4 43 43
megakaryocyte differentiation -0.055 0.14 -10000 0 -0.42 54 54
GSK3B -0.033 0.14 0.27 2 -0.4 44 46
RAF1 -0.017 0.12 0.23 4 -0.3 39 43
SHC1 0.019 0.009 -10000 0 -10000 0 0
STAT3 -0.053 0.14 -10000 0 -0.43 51 51
STAT1 -0.12 0.33 -10000 0 -0.83 78 78
HRAS/SPRED1 -0.01 0.12 0.23 1 -0.31 39 40
cell proliferation -0.054 0.15 -10000 0 -0.43 53 53
PIK3CA 0.02 0.018 -10000 0 -0.35 1 1
TEC 0.023 0.012 0.28 1 -10000 0 1
RPS6KB1 -0.049 0.16 -10000 0 -0.45 56 56
HRAS/SPRED2 -0.011 0.12 0.23 1 -0.31 38 39
LYN/TEC/p62DOK -0.02 0.15 -10000 0 -0.41 45 45
MAPK3 -0.013 0.097 0.23 7 -0.23 44 51
STAP1 -0.054 0.15 -10000 0 -0.43 51 51
GRAP2 0.011 0.062 -10000 0 -0.35 15 15
JAK2 -0.1 0.29 -10000 0 -0.73 75 75
STAT1 (dimer) -0.12 0.32 -10000 0 -0.81 78 78
mol:Gleevec 0.002 0.006 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.022 0.15 -10000 0 -0.42 45 45
actin filament polymerization -0.052 0.14 0.3 1 -0.42 51 52
LYN 0.021 0.007 -10000 0 -10000 0 0
STAP1/STAT5A (dimer) -0.084 0.22 -10000 0 -0.6 63 63
PIK3R1 0.018 0.037 -10000 0 -0.35 5 5
CBL/CRKL/GRB2 -0.032 0.14 -10000 0 -0.4 42 42
PI3K -0.025 0.16 -10000 0 -0.44 48 48
PTEN 0.021 0.006 -10000 0 -10000 0 0
SCF/KIT/EPO/EPOR -0.11 0.36 -10000 0 -1.1 49 49
MAPK8 -0.055 0.15 -10000 0 -0.44 53 53
STAT3 (dimer) -0.051 0.14 0.26 1 -0.42 51 52
positive regulation of transcription -0.008 0.083 0.2 9 -0.2 32 41
mol:GDP -0.034 0.12 -10000 0 -0.38 39 39
PIK3C2B -0.051 0.14 -10000 0 -0.43 47 47
CBL/CRKL -0.042 0.14 -10000 0 -0.41 47 47
FER -0.054 0.15 -10000 0 -0.43 53 53
SH2B3 -0.055 0.15 -10000 0 -0.43 52 52
PDPK1 -0.019 0.14 0.27 6 -0.37 40 46
SNAI2 -0.067 0.16 -10000 0 -0.45 60 60
positive regulation of cell proliferation -0.097 0.26 -10000 0 -0.64 78 78
KITLG -0.019 0.11 -10000 0 -0.37 48 48
cell motility -0.097 0.26 -10000 0 -0.64 78 78
PTPN6 0.024 0.018 0.33 1 -10000 0 1
EPOR -0.043 0.19 -10000 0 -0.72 21 21
STAT5A (dimer) -0.083 0.22 0.28 1 -0.6 63 64
SOCS1 0.021 0.017 -10000 0 -0.35 1 1
cell migration 0.056 0.14 0.42 53 -10000 0 53
SOS1 0.023 0.003 -10000 0 -10000 0 0
EPO 0.002 0.066 0.28 1 -0.36 15 16
VAV1 0.023 0.031 0.28 5 -0.35 1 6
GRB10 -0.056 0.15 -10000 0 -0.42 53 53
PTPN11 0.024 0.009 -10000 0 -10000 0 0
SCF/KIT -0.053 0.16 -10000 0 -0.44 53 53
GO:0007205 0.002 0.008 -10000 0 -10000 0 0
MAP2K1 -0.013 0.097 0.25 6 -0.24 38 44
CBL 0.022 0.005 -10000 0 -10000 0 0
KIT -0.1 0.34 -10000 0 -1.1 47 47
MAP2K2 -0.011 0.094 0.25 6 -0.24 36 42
SHC/Grb2/SOS1 -0.023 0.14 -10000 0 -0.41 42 42
STAT5A -0.084 0.23 -10000 0 -0.62 63 63
GRB2 0.022 0.006 -10000 0 -10000 0 0
response to radiation -0.065 0.16 0.29 2 -0.44 60 62
SHC/GRAP2 0.02 0.04 -10000 0 -0.24 10 10
PTPRO -0.056 0.15 -10000 0 -0.42 54 54
SH2B2 -0.054 0.14 -10000 0 -0.43 51 51
DOK1 0.023 0.003 -10000 0 -10000 0 0
MATK -0.056 0.15 -10000 0 -0.43 53 53
CREBBP 0.011 0.052 -10000 0 -0.18 9 9
BCL2 -0.14 0.4 -10000 0 -1.1 61 61
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

Figure S42.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S42.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MET/RANBP9 0.031 0.029 0.21 3 -0.24 4 7
CRKL -0.032 0.14 0.31 3 -0.5 26 29
mol:PIP3 -0.011 0.12 -10000 0 -0.78 12 12
AKT1 -0.01 0.11 0.35 2 -0.69 12 14
PTK2B 0.02 0.008 -10000 0 -10000 0 0
RAPGEF1 -0.033 0.13 0.29 4 -0.5 23 27
RANBP10 0.02 0.007 -10000 0 -10000 0 0
PIK3CA 0.02 0.018 -10000 0 -0.35 1 1
HGF/MET/SHIP2 -0.004 0.1 0.2 4 -0.21 99 103
MAP3K5 -0.025 0.13 0.29 5 -0.48 25 30
HGF/MET/CIN85/CBL/ENDOPHILINS 0.008 0.1 0.21 4 -0.19 98 102
AP1 -0.048 0.11 0.17 2 -0.22 147 149
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.019 0.009 -10000 0 -10000 0 0
apoptosis -0.21 0.35 -10000 0 -0.71 164 164
STAT3 (dimer) -0.026 0.091 -10000 0 -0.22 82 82
GAB1/CRKL/SHP2/PI3K -0.008 0.13 0.27 3 -0.46 23 26
INPP5D 0.022 0.017 -10000 0 -0.35 1 1
CBL/CRK -0.021 0.14 0.3 3 -0.51 23 26
PTPN11 0.023 0.003 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.022 0.005 -10000 0 -10000 0 0
PTEN 0.021 0.006 -10000 0 -10000 0 0
ELK1 0.011 0.1 0.3 45 -10000 0 45
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.02 0.075 -10000 0 -0.25 28 28
PAK1 -0.01 0.11 0.36 6 -0.66 12 18
HGF/MET/RANBP10 -0.006 0.1 0.2 4 -0.21 99 103
HRAS -0.037 0.14 -10000 0 -0.54 22 22
DOCK1 -0.031 0.14 0.32 8 -0.48 26 34
GAB1 -0.032 0.14 -10000 0 -0.54 25 25
CRK -0.03 0.14 0.3 3 -0.52 24 27
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP -0.067 0.18 -10000 0 -0.42 104 104
JUN 0.018 0.043 -10000 0 -0.35 7 7
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET -0.024 0.072 -10000 0 -0.17 97 97
PIK3R1 0.018 0.037 -10000 0 -0.35 5 5
cell morphogenesis -0.023 0.13 0.3 14 -0.38 25 39
GRB2/SHC -0.002 0.07 -10000 0 -0.16 75 75
FOS -0.087 0.17 -10000 0 -0.35 152 152
GLMN 0.003 0.001 -10000 0 -10000 0 0
cell motility 0.011 0.1 0.3 45 -10000 0 45
HGF/MET/MUC20 -0.014 0.096 0.19 4 -0.21 99 103
cell migration -0.002 0.069 -10000 0 -0.16 75 75
GRB2 0.022 0.006 -10000 0 -10000 0 0
CBL 0.022 0.005 -10000 0 -10000 0 0
MET/RANBP10 0.029 0.031 0.21 4 -0.24 4 8
HGF/MET/Paxillin/FAK1/FAK12/RasGAP -0.019 0.087 0.17 1 -0.21 85 86
MET/MUC20 0.016 0.027 0.19 4 -0.24 4 8
RAP1B -0.034 0.12 0.27 4 -0.48 22 26
RAP1A -0.035 0.12 0.27 4 -0.48 22 26
HGF/MET/RANBP9 -0.003 0.1 0.2 3 -0.21 95 98
RAF1 -0.034 0.13 -10000 0 -0.51 23 23
STAT3 -0.025 0.091 -10000 0 -0.22 81 81
cell proliferation -0.016 0.15 0.29 16 -0.31 70 86
RPS6KB1 -0.009 0.054 -10000 0 -0.28 13 13
MAPK3 0.007 0.14 0.7 17 -10000 0 17
MAPK1 0.019 0.16 0.68 26 -10000 0 26
RANBP9 0.022 0.004 -10000 0 -10000 0 0
MAPK8 -0.018 0.13 0.29 4 -0.45 29 33
SRC -0.027 0.079 0.15 1 -0.2 80 81
PI3K -0.003 0.078 -10000 0 -0.24 19 19
MET/Glomulin 0.016 0.03 0.21 4 -0.21 4 8
SOS1 0.023 0.003 -10000 0 -10000 0 0
MAP2K1 -0.032 0.13 -10000 0 -0.48 22 22
MET 0.021 0.04 0.28 4 -0.35 4 8
MAP4K1 -0.026 0.14 0.3 4 -0.52 24 28
PTK2 0.021 0.007 -10000 0 -10000 0 0
MAP2K2 -0.033 0.12 -10000 0 -0.48 22 22
BAD -0.009 0.11 0.4 4 -0.66 12 16
MAP2K4 -0.023 0.12 0.27 5 -0.43 25 30
SHP2/GRB2/SOS1/GAB1 -0.013 0.13 -10000 0 -0.46 24 24
INPPL1 0.023 0.003 -10000 0 -10000 0 0
PXN 0.023 0.003 -10000 0 -10000 0 0
SH3KBP1 0.023 0.003 -10000 0 -10000 0 0
HGS -0.026 0.064 -10000 0 -0.16 93 93
PLCgamma1/PKC 0.016 0.004 -10000 0 -10000 0 0
HGF -0.048 0.14 -10000 0 -0.35 98 98
RASA1 0.019 0.037 -10000 0 -0.35 5 5
NCK1 0.021 0.023 -10000 0 -0.35 2 2
PTPRJ 0.022 0.004 -10000 0 -10000 0 0
NCK/PLCgamma1 -0.004 0.084 -10000 0 -0.17 95 95
PDPK1 -0.011 0.11 0.24 1 -0.73 12 13
HGF/MET/SHIP -0.004 0.1 0.2 4 -0.21 99 103
Osteopontin-mediated events

Figure S43.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S43.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer 0.004 0.08 0.2 1 -0.17 66 67
NF kappa B1 p50/RelA/I kappa B alpha 0.001 0.093 0.34 5 -0.26 4 9
alphaV/beta3 Integrin/Osteopontin/Src 0.083 0.08 0.21 142 -10000 0 142
AP1 -0.044 0.14 -10000 0 -0.32 54 54
ILK -0.006 0.082 0.29 4 -0.21 2 6
bone resorption -0.019 0.082 0.25 4 -0.31 6 10
PTK2B 0.02 0.008 -10000 0 -10000 0 0
PYK2/p130Cas 0.042 0.11 0.26 1 -0.17 58 59
ITGAV 0.024 0.005 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 0.024 0.046 -10000 0 -0.24 14 14
alphaV/beta3 Integrin/Osteopontin 0.045 0.13 0.27 5 -0.2 84 89
MAP3K1 -0.008 0.083 0.21 9 -0.18 72 81
JUN 0.017 0.043 -10000 0 -0.35 7 7
MAPK3 -0.022 0.071 0.22 9 -10000 0 9
MAPK1 -0.022 0.072 0.21 9 -10000 0 9
Rac1/GDP 0.016 0.003 -10000 0 -10000 0 0
NFKB1 0.022 0.017 -10000 0 -0.35 1 1
MAPK8 -0.025 0.074 0.21 9 -0.24 7 16
ITGB3 -0.036 0.14 0.28 2 -0.35 85 87
NFKBIA -0.017 0.072 0.32 3 -0.22 2 5
FOS -0.087 0.17 -10000 0 -0.35 152 152
CD44 0.018 0.04 -10000 0 -0.35 6 6
CHUK 0.022 0.005 -10000 0 -10000 0 0
PLAU -0.025 0.1 0.61 1 -0.49 4 5
NF kappa B1 p50/RelA 0.019 0.083 0.31 3 -10000 0 3
BCAR1 0.02 0.007 -10000 0 -10000 0 0
RELA 0.022 0.004 -10000 0 -10000 0 0
alphaV beta3 Integrin -0.01 0.1 0.21 2 -0.24 85 87
mol:GDP 0 0 -10000 0 -10000 0 0
SYK -0.006 0.084 0.23 11 -0.18 70 81
VAV3 -0.011 0.083 0.25 11 -10000 0 11
MAP3K14 -0.006 0.083 0.21 9 -0.18 72 81
ROCK2 0.016 0.049 -10000 0 -0.35 9 9
SPP1 0.096 0.12 0.28 146 -10000 0 146
RAC1 0.022 0.005 -10000 0 -10000 0 0
Rac1/GTP -0.006 0.079 0.25 8 -10000 0 8
MMP2 -0.07 0.12 0.29 1 -0.33 53 54
Ephrin A reverse signaling

Figure S44.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S44.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAPKKK cascade 0.006 0.067 0.18 1 -0.2 47 48
EFNA5 0.013 0.065 0.28 2 -0.35 15 17
FYN -0.026 0.052 0.18 4 -0.19 44 48
neuron projection morphogenesis 0.006 0.067 0.18 1 -0.2 47 48
cell-cell signaling 0 0 -10000 0 -10000 0 0
Ephrin A5/EPHA5 0.007 0.067 0.19 1 -0.2 47 48
EPHA5 -0.004 0.089 -10000 0 -0.35 32 32
EPHB forward signaling

Figure S45.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S45.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Ephrin A5/EPHB2 0.024 0.042 0.19 4 -0.2 15 19
cell-cell adhesion 0.048 0.062 0.17 92 -10000 0 92
Ephrin B/EPHB2/RasGAP 0.032 0.081 -10000 0 -0.18 58 58
ITSN1 0.023 0.004 -10000 0 -10000 0 0
PIK3CA 0.02 0.018 -10000 0 -0.35 1 1
SHC1 0.019 0.009 -10000 0 -10000 0 0
Ephrin B1/EPHB3 0.029 0.04 0.19 14 -0.23 6 20
Ephrin B1/EPHB1 0.007 0.07 -10000 0 -0.2 51 51
HRAS/GDP -0.028 0.099 -10000 0 -0.23 57 57
Ephrin B/EPHB1/GRB7 0.016 0.11 0.23 16 -0.2 92 108
Endophilin/SYNJ1 -0.026 0.057 0.17 11 -0.32 1 12
KRAS 0.023 0.014 0.33 1 -10000 0 1
Ephrin B/EPHB1/Src 0.01 0.1 -10000 0 -0.19 94 94
endothelial cell migration 0.037 0.033 -10000 0 -0.18 8 8
GRB2 0.022 0.006 -10000 0 -10000 0 0
GRB7 0.038 0.074 0.32 30 -0.35 2 32
PAK1 -0.026 0.072 0.26 6 -0.32 3 9
HRAS 0.022 0.005 -10000 0 -10000 0 0
RRAS -0.027 0.056 0.17 9 -0.32 1 10
DNM1 0.018 0.04 -10000 0 -0.35 6 6
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.038 0.08 0.18 19 -0.18 92 111
lamellipodium assembly -0.048 0.062 -10000 0 -0.17 92 92
Ephrin B/EPHB1/Src/p52 SHC/GRB2 -0.015 0.082 -10000 0 -0.21 49 49
PIK3R1 0.018 0.037 -10000 0 -0.35 5 5
EPHB2 0.024 0.02 0.28 3 -10000 0 3
EPHB3 0.024 0.06 0.28 15 -0.35 6 21
EPHB1 -0.014 0.11 -10000 0 -0.35 50 50
EPHB4 0.022 0.004 -10000 0 -10000 0 0
mol:GDP -0.04 0.085 0.27 2 -0.24 51 53
Ephrin B/EPHB2 0.025 0.072 0.19 2 -0.18 53 55
Ephrin B/EPHB3 0.024 0.075 0.2 7 -0.19 49 56
JNK cascade -0.022 0.083 0.28 21 -0.18 50 71
Ephrin B/EPHB1 0.003 0.095 -10000 0 -0.19 94 94
RAP1/GDP -0.028 0.1 0.24 5 -0.28 23 28
EFNB2 0.02 0.029 -10000 0 -0.35 3 3
EFNB3 -0.015 0.11 -10000 0 -0.35 50 50
EFNB1 0.022 0.016 -10000 0 -0.35 1 1
Ephrin B2/EPHB1-2 0.018 0.071 0.19 3 -0.18 53 56
RAP1B 0.023 0.002 -10000 0 -10000 0 0
RAP1A 0.023 0.001 -10000 0 -10000 0 0
CDC42/GTP -0.009 0.098 -10000 0 -0.23 53 53
Rap1/GTP -0.052 0.064 -10000 0 -0.18 94 94
axon guidance 0.024 0.042 0.18 4 -0.2 15 19
MAPK3 -0.022 0.074 0.18 4 -0.28 12 16
MAPK1 -0.021 0.07 0.17 2 -0.28 9 11
Rac1/GDP -0.038 0.094 0.36 1 -0.27 30 31
actin cytoskeleton reorganization -0.054 0.06 -10000 0 -0.2 51 51
CDC42/GDP -0.035 0.097 0.24 6 -0.27 30 36
PI3K 0.041 0.035 -10000 0 -0.18 8 8
EFNA5 0.013 0.065 0.28 2 -0.35 15 17
Ephrin B2/EPHB4 0.027 0.02 -10000 0 -0.2 3 3
Ephrin B/EPHB2/Intersectin/N-WASP -0.007 0.073 0.17 1 -0.2 53 54
CDC42 0.022 0.004 -10000 0 -10000 0 0
RAS family/GTP -0.051 0.062 -10000 0 -0.29 9 9
PTK2 0.045 0.16 0.55 47 -10000 0 47
MAP4K4 -0.022 0.083 0.29 21 -0.18 50 71
SRC 0.022 0.005 -10000 0 -10000 0 0
KALRN 0.019 0.037 -10000 0 -0.35 5 5
Intersectin/N-WASP 0.032 0.009 -10000 0 -10000 0 0
neuron projection morphogenesis -0.035 0.099 0.31 19 -0.29 11 30
MAP2K1 -0.018 0.075 -10000 0 -0.2 47 47
WASL 0.022 0.005 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 0.031 0.077 0.21 2 -0.19 52 54
cell migration -0.018 0.11 0.27 8 -0.33 16 24
NRAS 0.023 0.001 -10000 0 -10000 0 0
SYNJ1 -0.027 0.057 0.17 11 -0.32 1 12
PXN 0.023 0.003 -10000 0 -10000 0 0
TF -0.031 0.06 0.17 9 -0.31 2 11
HRAS/GTP -0.003 0.088 -10000 0 -0.18 94 94
Ephrin B1/EPHB1-2 0.02 0.07 0.19 2 -0.19 51 53
cell adhesion mediated by integrin 0.017 0.061 0.18 46 -0.22 5 51
RAC1 0.022 0.005 -10000 0 -10000 0 0
mol:GTP -0.002 0.091 -10000 0 -0.18 95 95
RAC1-CDC42/GTP -0.049 0.066 -10000 0 -0.18 84 84
RASA1 0.019 0.037 -10000 0 -0.35 5 5
RAC1-CDC42/GDP -0.029 0.096 0.35 1 -0.28 23 24
ruffle organization -0.037 0.092 0.34 10 -0.3 9 19
NCK1 0.021 0.023 -10000 0 -0.35 2 2
receptor internalization -0.03 0.06 0.16 11 -0.32 5 16
Ephrin B/EPHB2/KALRN 0.031 0.082 -10000 0 -0.19 56 56
ROCK1 0.003 0.059 0.18 43 -0.21 6 49
RAS family/GDP -0.055 0.062 -10000 0 -0.2 52 52
Rac1/GTP -0.05 0.065 -10000 0 -0.18 92 92
Ephrin B/EPHB1/Src/Paxillin -0.024 0.093 -10000 0 -0.21 98 98
Ras signaling in the CD4+ TCR pathway

Figure S46.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S46.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ERK1-2/ELK1 -0.09 0.2 -10000 0 -0.54 47 47
MAP3K8 0.01 0.033 -10000 0 -0.35 3 3
FOS -0.061 0.16 -10000 0 -0.48 43 43
PRKCA -0.012 0.087 -10000 0 -0.35 30 30
PTPN7 0.009 0.036 0.26 6 -10000 0 6
HRAS 0.021 0.005 -10000 0 -10000 0 0
PRKCB -0.013 0.088 -10000 0 -0.35 31 31
NRAS 0.022 0.002 -10000 0 -10000 0 0
RAS family/GTP 0.023 0.033 0.22 1 -10000 0 1
MAPK3 -0.029 0.14 -10000 0 -0.68 16 16
MAP2K1 -0.059 0.15 -10000 0 -0.4 70 70
ELK1 0.006 0.027 -10000 0 -10000 0 0
BRAF -0.041 0.13 -10000 0 -0.36 61 61
mol:GTP -0.001 0.002 -10000 0 -0.005 157 157
MAPK1 -0.036 0.14 -10000 0 -0.59 23 23
RAF1 -0.041 0.13 -10000 0 -0.38 59 59
KRAS 0.022 0.014 0.33 1 -10000 0 1
S1P1 pathway

Figure S47.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S47.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer 0.014 0.066 -10000 0 -0.25 29 29
PDGFRB 0.006 0.071 -10000 0 -0.36 19 19
SPHK1 -0.019 0.12 -10000 0 -0.78 12 12
mol:S1P -0.022 0.11 -10000 0 -0.68 12 12
S1P1/S1P/Gi -0.1 0.19 0.24 1 -0.44 95 96
GNAO1 -0.069 0.16 -10000 0 -0.35 120 120
PDGFB-D/PDGFRB/PLCgamma1 -0.085 0.18 0.28 4 -0.4 94 98
PLCG1 -0.096 0.18 0.27 3 -0.42 90 93
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.006 0.071 -10000 0 -0.36 19 19
GNAI2 0.018 0.015 -10000 0 -10000 0 0
GNAI3 0.018 0.015 -10000 0 -10000 0 0
GNAI1 0.012 0.048 -10000 0 -0.36 8 8
mol:GDP 0 0 -10000 0 -10000 0 0
EDG1 -0.018 0.047 -10000 0 -0.2 29 29
S1P1/S1P -0.027 0.096 0.22 2 -0.42 16 18
negative regulation of cAMP metabolic process -0.1 0.19 0.24 1 -0.42 95 96
MAPK3 -0.12 0.22 0.25 4 -0.54 87 91
calcium-dependent phospholipase C activity -0.001 0.003 -10000 0 -10000 0 0
Rac1/GDP 0.016 0.003 -10000 0 -10000 0 0
RhoA/GDP 0.016 0.004 -10000 0 -10000 0 0
KDR -0.001 0.087 -10000 0 -0.35 30 30
PLCB2 -0.019 0.089 0.22 5 -0.38 14 19
RAC1 0.022 0.005 -10000 0 -10000 0 0
RhoA/GTP -0.022 0.081 -10000 0 -0.35 16 16
receptor internalization -0.027 0.088 -10000 0 -0.39 16 16
PTGS2 -0.15 0.31 0.37 1 -0.91 65 66
Rac1/GTP -0.022 0.082 -10000 0 -0.35 16 16
RHOA 0.022 0.005 -10000 0 -10000 0 0
VEGFA 0.021 0.011 -10000 0 -10000 0 0
negative regulation of T cell proliferation -0.1 0.19 0.24 1 -0.42 95 96
GO:0007205 0 0 -10000 0 -10000 0 0
GNAZ 0.007 0.064 -10000 0 -0.36 15 15
MAPK1 -0.12 0.22 0.23 1 -0.55 85 86
S1P1/S1P/PDGFB-D/PDGFRB -0.023 0.11 0.25 5 -0.37 24 29
ABCC1 0.018 0.014 -10000 0 -10000 0 0
Arf6 signaling events

Figure S48.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S48.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CENTA1/KIF3B 0.026 0.012 -10000 0 -10000 0 0
ARNO/beta Arrestin1-2 -0.008 0.12 -10000 0 -0.77 8 8
EGFR 0.014 0.06 0.33 1 -0.35 13 14
EPHA2 0.022 0.005 -10000 0 -10000 0 0
USP6 0.021 0.006 -10000 0 -10000 0 0
IQSEC1 0.022 0.017 -10000 0 -0.35 1 1
EGFR/EGFR/EGF/EGF 0.032 0.057 0.21 20 -0.24 13 33
ARRB2 0.007 0.002 -10000 0 -10000 0 0
mol:GTP 0.011 0.049 0.13 24 -0.16 12 36
ARRB1 0.021 0.023 -10000 0 -0.35 2 2
FBXO8 0.022 0.004 -10000 0 -10000 0 0
TSHR 0.025 0.057 0.28 18 -0.35 3 21
EGF 0.03 0.053 0.28 20 -0.35 1 21
somatostatin receptor activity 0 0 0.001 6 -0.001 74 80
ARAP2 0.02 0.028 -10000 0 -0.35 3 3
mol:GDP -0.061 0.12 0.18 5 -0.27 89 94
mol:PI-3-4-5-P3 0 0 0.001 4 -0.001 46 50
ITGA2B 0.019 0.038 0.28 1 -0.35 5 6
ARF6 0.023 0.003 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.043 0.031 -10000 0 -0.19 2 2
ADAP1 0.022 0.005 -10000 0 -10000 0 0
KIF13B 0.02 0.008 -10000 0 -10000 0 0
HGF/MET -0.02 0.11 0.21 4 -0.25 99 103
PXN 0.023 0.003 -10000 0 -10000 0 0
ARF6/GTP -0.059 0.11 0.22 6 -0.26 80 86
EGFR/EGFR/EGF/EGF/ARFGEP100 0.041 0.053 0.2 19 -0.21 14 33
ADRB2 -0.043 0.14 -10000 0 -0.35 90 90
receptor agonist activity 0 0 0 3 0 72 75
actin filament binding 0 0 0 5 0 78 83
SRC 0.022 0.005 -10000 0 -10000 0 0
ITGB3 -0.038 0.14 0.28 2 -0.35 85 87
GNAQ 0.021 0.017 -10000 0 -0.35 1 1
EFA6/PI-4-5-P2 0 0 0.001 12 -0.001 49 61
ARF6/GDP -0.014 0.14 0.24 12 -0.41 43 55
ARF6/GDP/GULP/ACAP1 -0.057 0.14 0.2 1 -0.33 72 73
alphaIIb/beta3 Integrin/paxillin/GIT1 0.014 0.093 0.21 3 -0.19 86 89
ACAP1 0.022 0.026 0.28 3 -0.35 1 4
ACAP2 0.02 0.018 -10000 0 -0.35 1 1
LHCGR/beta Arrestin2 0.011 0.018 -10000 0 -10000 0 0
EFNA1 0.02 0.02 0.3 2 -10000 0 2
HGF -0.048 0.15 -10000 0 -0.35 98 98
CYTH3 -0.006 0.001 -10000 0 -10000 0 0
CYTH2 0 0.12 -10000 0 -0.99 8 8
NCK1 0.021 0.023 -10000 0 -0.35 2 2
fibronectin binding 0 0 0.001 7 0 62 69
endosomal lumen acidification 0 0 0.001 10 0 54 64
microtubule-based process 0 0 -10000 0 -10000 0 0
GULP1 -0.018 0.12 -10000 0 -0.35 57 57
GNAQ/ARNO 0.012 0.12 -10000 0 -0.92 8 8
mol:Phosphatidic acid 0 0 0 1 -10000 0 1
PIP3-E 0 0 0 6 0 11 17
MET 0.021 0.04 0.28 4 -0.35 4 8
GNA14 -0.01 0.1 -10000 0 -0.35 44 44
GNA15 0.025 0.03 0.28 7 -10000 0 7
GIT1 0.022 0.005 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 0.001 9 -0.001 56 65
GNA11 0.015 0.049 -10000 0 -0.35 9 9
LHCGR 0.004 0.017 -10000 0 -10000 0 0
AGTR1 -0.059 0.15 0.28 2 -0.35 106 108
desensitization of G-protein coupled receptor protein signaling pathway 0.011 0.018 -10000 0 -10000 0 0
IPCEF1/ARNO 0.023 0.12 -10000 0 -0.84 8 8
alphaIIb/beta3 Integrin -0.015 0.11 0.21 3 -0.24 90 93
IL4-mediated signaling events

Figure S49.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S49.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.083 0.46 0.67 1 -1.1 47 48
STAT6 (cleaved dimer) -0.1 0.44 0.56 2 -1 58 60
IGHG1 0.006 0.22 0.4 10 -0.82 5 15
IGHG3 -0.095 0.44 0.59 1 -1 54 55
AKT1 -0.023 0.27 0.5 3 -0.8 13 16
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 0.009 0.22 0.48 3 -0.85 8 11
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.027 0.28 0.53 2 -0.74 23 25
THY1 -0.092 0.46 0.67 1 -1.1 48 49
MYB 0.046 0.074 0.28 47 -10000 0 47
HMGA1 0.059 0.09 0.28 71 -10000 0 71
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.018 0.31 0.56 5 -0.67 32 37
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.009 0.27 0.52 3 -0.82 12 15
SP1 0.025 0.013 -10000 0 -10000 0 0
INPP5D 0.022 0.017 -10000 0 -0.35 1 1
SOCS5 0.004 0.037 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.096 0.45 0.6 1 -1.1 52 53
SOCS1 -0.045 0.32 0.51 2 -0.71 43 45
SOCS3 -0.014 0.27 0.52 2 -0.76 14 16
FCER2 -0.071 0.4 0.72 2 -0.94 43 45
PARP14 0.023 0.006 -10000 0 -10000 0 0
CCL17 -0.088 0.46 0.74 2 -1.1 48 50
GRB2 0.022 0.006 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP 0.015 0.23 0.46 5 -0.65 10 15
T cell proliferation -0.11 0.45 0.64 1 -1.1 52 53
IL4R/JAK1 -0.1 0.45 -10000 0 -1.1 51 51
EGR2 -0.12 0.53 0.7 2 -1.3 55 57
JAK2 0.011 0.081 -10000 0 -0.36 9 9
JAK3 0.023 0.028 0.3 4 -10000 0 4
PIK3R1 0.018 0.037 -10000 0 -0.35 5 5
JAK1 0.017 0.037 -10000 0 -0.34 1 1
COL1A2 0.001 0.23 -10000 0 -1.3 6 6
CCL26 -0.093 0.46 0.67 1 -1.1 46 47
IL4R -0.094 0.49 0.71 3 -1.2 51 54
PTPN6 0.008 0.035 0.34 1 -10000 0 1
IL13RA2 -0.087 0.46 0.67 1 -1.1 47 48
IL13RA1 0.018 0.066 -10000 0 -10000 0 0
IRF4 0.001 0.25 0.51 2 -0.99 20 22
ARG1 0.016 0.18 0.46 1 -0.65 3 4
CBL -0.022 0.28 0.5 5 -0.65 29 34
GTF3A 0.025 0.008 -10000 0 -10000 0 0
PIK3CA 0.02 0.018 -10000 0 -0.35 1 1
IL13RA1/JAK2 0.03 0.1 0.22 10 -0.26 7 17
IRF4/BCL6 0 0.22 -10000 0 -0.95 19 19
CD40LG 0.017 0.059 -10000 0 -0.29 16 16
MAPK14 -0.02 0.29 0.52 4 -0.67 27 31
mitosis -0.019 0.26 0.49 3 -0.75 13 16
STAT6 -0.097 0.53 0.76 4 -1.2 52 56
SPI1 0.025 0.02 0.28 3 -10000 0 3
RPS6KB1 -0.016 0.25 0.47 3 -0.72 13 16
STAT6 (dimer) -0.096 0.53 0.77 4 -1.2 52 56
STAT6 (dimer)/PARP14 -0.11 0.47 0.62 2 -1.1 53 55
mast cell activation -0.002 0.018 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.014 0.27 0.54 4 -0.76 17 21
FRAP1 -0.023 0.27 0.5 3 -0.8 13 16
LTA -0.09 0.46 0.69 2 -1.1 47 49
FES 0.022 0.017 -10000 0 -0.35 1 1
T-helper 1 cell differentiation 0.092 0.52 1.2 52 -0.76 4 56
CCL11 -0.11 0.46 -10000 0 -1.1 56 56
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.007 0.26 0.53 3 -0.83 11 14
IL2RG 0.023 0.043 0.29 6 -0.35 3 9
IL10 -0.061 0.47 0.76 10 -1.1 40 50
IRS1 -0.013 0.11 -10000 0 -0.35 50 50
IRS2 -0.026 0.12 -10000 0 -0.35 67 67
IL4 0.015 0.21 -10000 0 -0.95 9 9
IL5 -0.097 0.46 0.67 1 -1.1 51 52
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.054 0.41 0.66 4 -0.9 47 51
COL1A1 -0.016 0.29 0.48 2 -0.92 22 24
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.11 0.46 -10000 0 -1.2 44 44
IL2R gamma/JAK3 0.036 0.045 0.31 7 -0.25 3 10
TFF3 -0.093 0.53 0.72 2 -1.2 62 64
ALOX15 -0.075 0.47 0.72 2 -1.1 48 50
MYBL1 0.021 0.007 -10000 0 -10000 0 0
T-helper 2 cell differentiation -0.094 0.42 0.64 2 -0.94 57 59
SHC1 0.019 0.009 -10000 0 -10000 0 0
CEBPB 0.023 0.007 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.029 0.27 0.49 3 -0.78 16 19
mol:PI-3-4-5-P3 -0.022 0.27 0.5 3 -0.8 13 16
PI3K -0.026 0.28 0.59 1 -0.88 13 14
DOK2 0.022 0.021 0.28 3 -10000 0 3
ETS1 0 0.04 -10000 0 -0.33 1 1
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 0.019 0.21 0.41 11 -0.59 10 21
ITGB3 -0.22 0.61 0.67 1 -1.2 112 113
PIGR -0.094 0.56 0.77 10 -1.2 67 77
IGHE -0.001 0.07 0.18 25 -0.17 6 31
MAPKKK cascade 0.02 0.21 0.4 11 -0.58 10 21
BCL6 0.019 0.019 -10000 0 -0.35 1 1
OPRM1 -0.094 0.46 0.68 2 -1.1 47 49
RETNLB -0.094 0.46 0.68 2 -1.1 47 49
SELP -0.3 0.7 0.76 9 -1.2 183 192
AICDA -0.096 0.44 0.64 2 -1.1 48 50
Glucocorticoid receptor regulatory network

Figure S50.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S50.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PCK2 -0.048 0.069 -10000 0 -0.37 5 5
SMARCC2 0.023 0.006 -10000 0 -10000 0 0
SMARCC1 0.022 0.007 -10000 0 -10000 0 0
TBX21 0.056 0.13 0.39 6 -0.65 10 16
SUMO2 0.018 0.014 -10000 0 -10000 0 0
STAT1 (dimer) 0.026 0.012 0.28 1 -10000 0 1
FKBP4 0.022 0.004 -10000 0 -10000 0 0
FKBP5 0.018 0.043 -10000 0 -0.35 7 7
GR alpha/HSP90/FKBP51/HSP90 -0.065 0.1 0.26 2 -0.26 69 71
PRL 0.022 0.23 0.4 24 -1.1 18 42
cortisol/GR alpha (dimer)/TIF2 -0.12 0.16 0.42 6 -0.37 56 62
RELA 0.014 0.079 -10000 0 -0.22 27 27
FGG -0.12 0.15 0.38 6 -0.34 70 76
GR beta/TIF2 -0.083 0.11 0.27 2 -0.3 75 77
IFNG 0.091 0.15 0.42 10 -0.45 4 14
apoptosis -0.12 0.2 0.52 7 -0.52 64 71
CREB1 0.031 0.023 -10000 0 -10000 0 0
histone acetylation 0.036 0.071 0.22 2 -0.25 3 5
BGLAP 0.087 0.096 0.35 7 -10000 0 7
GR/PKAc -0.056 0.098 0.25 2 -0.24 61 63
NF kappa B1 p50/RelA 0.027 0.14 0.25 1 -0.31 66 67
SMARCD1 0.023 0.006 -10000 0 -10000 0 0
MDM2 -0.024 0.048 0.17 5 -0.13 1 6
GATA3 0.026 0.058 0.28 13 -0.35 6 19
AKT1 0.02 0.004 -10000 0 -10000 0 0
CSF2 0.023 0.055 -10000 0 -10000 0 0
GSK3B 0.019 0.014 -10000 0 -10000 0 0
NR1I3 -0.077 0.19 0.51 8 -0.51 34 42
CSN2 -0.12 0.13 0.3 6 -0.31 77 83
BRG1/BAF155/BAF170/BAF60A 0.054 0.025 -10000 0 -0.14 2 2
NFATC1 0.014 0.058 -10000 0 -0.35 13 13
POU2F1 0.013 0.05 -10000 0 -0.27 15 15
CDKN1A 0.014 0.07 -10000 0 -1 1 1
response to stress 0 0 -10000 0 -10000 0 0
response to UV -0.001 0.007 -10000 0 -10000 0 0
SFN 0.21 0.12 0.28 372 -10000 0 372
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.059 0.15 0.28 26 -0.23 61 87
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.15 0.27 0.48 7 -0.75 74 81
JUN 0.097 0.11 0.29 52 -0.38 3 55
IL4 0.055 0.08 -10000 0 -10000 0 0
CDK5R1 0.021 0.015 0.28 1 -10000 0 1
PRKACA 0.022 0.005 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.11 0.1 -10000 0 -0.25 132 132
GR alpha/HSP90/FKBP51/HSP90/PP5C -0.054 0.1 0.26 2 -0.24 63 65
cortisol/GR alpha (monomer) -0.15 0.18 0.46 9 -0.4 71 80
NCOA2 0.009 0.064 -10000 0 -0.35 16 16
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.038 0.19 0.2 8 -0.33 150 158
AP-1/NFAT1-c-4 0.1 0.19 0.4 57 -0.46 12 69
AFP 0.073 0.091 -10000 0 -10000 0 0
SUV420H1 0.022 0.004 -10000 0 -10000 0 0
IRF1 -0.064 0.09 0.34 1 -0.35 1 2
TP53 0.028 0.039 -10000 0 -0.83 1 1
PPP5C 0.023 0.004 -10000 0 -10000 0 0
KRT17 0.095 0.2 0.39 63 -0.85 10 73
KRT14 0.099 0.12 0.44 6 -10000 0 6
TBP 0.026 0.005 -10000 0 -10000 0 0
CREBBP -0.009 0.048 -10000 0 -0.25 1 1
HDAC1 0.022 0.004 -10000 0 -10000 0 0
HDAC2 0.022 0.007 -10000 0 -10000 0 0
AP-1 0.1 0.19 0.4 58 -0.47 12 70
MAPK14 0.019 0.014 -10000 0 -10000 0 0
MAPK10 -0.058 0.15 -10000 0 -0.35 107 107
MAPK11 0.016 0.027 -10000 0 -0.35 2 2
KRT5 0.11 0.22 0.41 51 -0.91 11 62
interleukin-1 receptor activity -0.001 0.002 -10000 0 -10000 0 0
NCOA1 0.022 0.017 -10000 0 -0.35 1 1
STAT1 0.026 0.012 0.28 1 -10000 0 1
CGA 0.076 0.089 0.34 12 -10000 0 12
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 -0.089 0.11 0.29 1 -0.36 30 31
MAPK3 0.018 0.016 -10000 0 -10000 0 0
MAPK1 0.018 0.015 -10000 0 -10000 0 0
ICAM1 0.064 0.13 0.34 8 -0.4 7 15
NFKB1 0.011 0.084 -10000 0 -0.21 39 39
MAPK8 0.11 0.11 0.28 69 -0.26 5 74
MAPK9 0.018 0.014 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) -0.12 0.21 0.53 7 -0.54 65 72
BAX 0.012 0.059 -10000 0 -0.46 1 1
POMC 0.058 0.21 0.51 11 -1.1 11 22
EP300 -0.01 0.048 -10000 0 -0.25 1 1
cortisol/GR alpha (dimer)/p53 -0.12 0.16 0.43 8 -0.38 37 45
proteasomal ubiquitin-dependent protein catabolic process -0.028 0.043 0.23 4 -10000 0 4
SGK1 -0.037 0.12 -10000 0 -1.1 3 3
IL13 0.066 0.13 0.44 1 -0.45 4 5
IL6 0.043 0.2 0.35 8 -0.81 18 26
PRKACG 0.017 0.005 -10000 0 -10000 0 0
IL5 0.057 0.11 0.38 1 -0.54 2 3
IL2 0.073 0.15 0.38 3 -0.46 8 11
CDK5 0.021 0.008 -10000 0 -10000 0 0
PRKACB 0.019 0.04 -10000 0 -0.35 6 6
HSP90AA1 0.022 0.004 -10000 0 -10000 0 0
IL8 0.095 0.15 0.33 36 -0.38 6 42
CDK5R1/CDK5 0.027 0.02 0.21 1 -10000 0 1
NF kappa B1 p50/RelA/PKAc 0.048 0.12 -10000 0 -0.28 38 38
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 -0.11 0.15 0.42 8 -0.35 40 48
SMARCA4 0.021 0.008 -10000 0 -10000 0 0
chromatin remodeling -0.069 0.1 0.3 4 -0.34 16 20
NF kappa B1 p50/RelA/Cbp 0.011 0.13 -10000 0 -0.33 29 29
JUN (dimer) 0.096 0.11 0.29 52 -0.38 3 55
YWHAH 0.022 0.006 -10000 0 -10000 0 0
VIPR1 0.066 0.093 0.33 10 -0.57 3 13
NR3C1 -0.12 0.15 0.3 6 -0.39 75 81
NR4A1 -0.007 0.12 -10000 0 -0.4 42 42
TIF2/SUV420H1 0.021 0.049 -10000 0 -0.24 16 16
MAPKKK cascade -0.12 0.2 0.52 7 -0.52 64 71
cortisol/GR alpha (dimer)/Src-1 -0.12 0.16 0.42 9 -0.36 49 58
PBX1 0.001 0.084 -10000 0 -0.34 29 29
POU1F1 0.011 0.059 0.28 2 -0.29 17 19
SELE -0.01 0.31 0.34 9 -0.81 62 71
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A -0.069 0.11 0.3 4 -0.34 16 20
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 -0.11 0.15 0.42 8 -0.35 40 48
mol:cortisol -0.066 0.091 0.26 7 -0.21 41 48
MMP1 0.11 0.16 0.36 17 -0.48 12 29
Visual signal transduction: Rods

Figure S51.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S51.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:K + 0.022 0.005 -10000 0 -10000 0 0
GNAT1/GTP 0.016 0.018 0.19 5 -10000 0 5
Metarhodopsin II/Arrestin 0.026 0.014 0.19 3 -10000 0 3
PDE6G/GNAT1/GTP 0.037 0.043 0.19 37 -0.2 1 38
mol:GTP 0 0 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
GNAT1 0.022 0.026 0.28 5 -10000 0 5
GRK1 0.018 0.013 0.28 1 -10000 0 1
CNG Channel 0.037 0.058 0.23 7 -0.17 22 29
mol:Na + 0.04 0.045 0.27 3 -0.18 6 9
mol:ADP 0.018 0.013 0.28 1 -10000 0 1
RGS9-1/Gbeta5/R9AP -0.007 0.11 0.21 14 -0.21 108 122
mol:GDP 0 0 -10000 0 -10000 0 0
cGMP/CNG Channel 0.05 0.052 0.32 3 -0.18 6 9
CNGB1 0.03 0.052 0.28 21 -10000 0 21
RDH5 0.024 0.02 0.28 3 -10000 0 3
SAG 0.019 0.004 -10000 0 -10000 0 0
mol:Ca2+ -0.015 0.065 0.34 13 -10000 0 13
Na + (4 Units) 0.03 0.039 0.2 3 -0.17 6 9
RGS9 -0.057 0.15 -10000 0 -0.35 110 110
GNB1/GNGT1 0.09 0.084 0.21 172 -10000 0 172
GNAT1/GDP 0.001 0.097 0.2 12 -0.18 108 120
GUCY2D 0.025 0.036 0.28 10 -10000 0 10
GNGT1 0.11 0.12 0.28 181 -10000 0 181
GUCY2F 0.019 0.003 -10000 0 -10000 0 0
GNB5 0.022 0.005 -10000 0 -10000 0 0
mol:GMP (4 units) 0.015 0.048 0.17 10 -0.18 22 32
mol:11-cis-retinal 0.024 0.02 0.28 3 -10000 0 3
mol:cGMP 0.038 0.039 0.25 1 -0.18 6 7
GNB1 0.022 0.004 -10000 0 -10000 0 0
Rhodopsin 0.032 0.019 0.21 5 -10000 0 5
SLC24A1 0.022 0.005 -10000 0 -10000 0 0
CNGA1 0.029 0.042 0.28 14 -10000 0 14
Metarhodopsin II 0.023 0.015 0.18 4 -10000 0 4
mol:Ca ++ 0 0 -10000 0 -10000 0 0
GC1/GCAP Family 0.05 0.046 0.35 1 -0.19 6 7
RGS9BP 0.033 0.057 0.29 23 -10000 0 23
Metarhodopsin II/Transducin 0.035 0.043 0.16 25 -10000 0 25
GCAP Family/Ca ++ 0.039 0.036 0.19 15 -0.19 6 21
PDE6A/B 0.022 0.057 0.21 4 -0.24 21 25
mol:Pi -0.008 0.11 0.21 14 -0.21 108 122
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
Transducin 0.086 0.075 0.2 161 -10000 0 161
PDE6B 0.008 0.075 0.28 2 -0.35 21 23
PDE6A 0.024 0.023 0.28 4 -10000 0 4
PDE6G 0.042 0.074 0.28 42 -0.35 1 43
RHO 0.02 0.02 0.28 3 -10000 0 3
PDE6 0.009 0.12 0.28 9 -0.19 121 130
GUCA1A 0.029 0.046 0.28 17 -10000 0 17
GC2/GCAP Family 0.05 0.039 -10000 0 -0.2 6 6
GUCA1C 0.016 0.002 -10000 0 -10000 0 0
GUCA1B 0.018 0.04 -10000 0 -0.35 6 6
Lissencephaly gene (LIS1) in neuronal migration and development

Figure S52.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S52.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
DYNC1H1 0.022 0.004 -10000 0 -10000 0 0
VLDLR 0.021 0.024 -10000 0 -0.35 2 2
LRPAP1 0.022 0.004 -10000 0 -10000 0 0
NUDC 0.022 0.005 -10000 0 -10000 0 0
RELN/LRP8 -0.038 0.12 0.23 7 -0.21 171 178
CaM/Ca2+ 0.017 0.003 -10000 0 -10000 0 0
KATNA1 0.023 0.003 -10000 0 -10000 0 0
GO:0030286 0 0 -10000 0 -10000 0 0
ABL1 -0.064 0.09 0.18 12 -0.19 162 174
IQGAP1/CaM 0.032 0.008 -10000 0 -10000 0 0
DAB1 0.027 0.041 0.28 13 -10000 0 13
IQGAP1 0.022 0.004 -10000 0 -10000 0 0
PLA2G7 0.02 0.038 0.28 1 -0.35 5 6
CALM1 0.022 0.004 -10000 0 -10000 0 0
DYNLT1 0.022 0.004 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
LRPAP1/LRP8 0.035 0.019 0.21 5 -10000 0 5
UniProt:Q4QZ09 0 0 -10000 0 -10000 0 0
CLIP1 0.023 0.003 -10000 0 -10000 0 0
CDK5R1 0.022 0.013 0.28 1 -10000 0 1
LIS1/Poliovirus Protein 3A -0.008 0.003 -10000 0 -10000 0 0
CDK5R2 0.048 0.079 0.28 54 -10000 0 54
mol:PP1 0 0 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 -0.037 0.12 0.22 15 -0.21 170 185
YWHAE 0.021 0.007 -10000 0 -10000 0 0
NDEL1/14-3-3 E -0.041 0.096 0.29 11 -0.22 5 16
MAP1B -0.006 0.048 -10000 0 -0.23 23 23
RAC1 0.008 0.003 -10000 0 -10000 0 0
p35/CDK5 -0.064 0.08 0.18 9 -10000 0 9
RELN -0.1 0.18 0.28 6 -0.35 174 180
PAFAH/LIS1 0.019 0.025 0.2 1 -0.21 5 6
LIS1/CLIP170 0.021 0.008 -10000 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.036 0.08 -10000 0 -0.2 1 1
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.049 0.11 0.25 2 -0.28 14 16
GO:0005869 0 0 -10000 0 -10000 0 0
NDEL1 -0.049 0.084 0.29 4 -0.22 3 7
LIS1/IQGAP1 0.021 0.008 -10000 0 -10000 0 0
RHOA 0.008 0.003 -10000 0 -10000 0 0
PAFAH1B1 -0.011 0.004 -10000 0 -10000 0 0
PAFAH1B3 0.027 0.034 0.28 9 -10000 0 9
PAFAH1B2 0.022 0.017 -10000 0 -0.35 1 1
MAP1B/LIS1/Dynein heavy chain 0.009 0.041 -10000 0 -0.16 21 21
NDEL1/Katanin 60/Dynein heavy chain -0.031 0.1 0.3 9 -0.22 7 16
LRP8 0.025 0.026 0.29 5 -10000 0 5
NDEL1/Katanin 60 -0.043 0.095 0.29 10 -0.22 8 18
P39/CDK5 -0.051 0.1 0.18 43 -0.18 54 97
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.021 0.008 -10000 0 -10000 0 0
CDK5 -0.063 0.083 0.18 10 -0.18 161 171
PPP2R5D 0.023 0.004 -10000 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0.018 0.007 -10000 0 -10000 0 0
CSNK2A1 0.022 0.004 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 -0.029 0.11 0.21 11 -0.18 166 177
RELN/VLDLR -0.026 0.12 0.21 6 -0.19 168 174
CDC42 0.008 0.003 -10000 0 -10000 0 0
HIF-2-alpha transcription factor network

Figure S53.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S53.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MMP14 -0.004 0.089 -10000 0 -0.59 10 10
oxygen homeostasis -0.008 0.013 -10000 0 -10000 0 0
TCEB2 0.022 0.005 -10000 0 -10000 0 0
TCEB1 0.021 0.007 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/HIF2A -0.001 0.092 -10000 0 -0.25 7 7
EPO -0.085 0.17 -10000 0 -0.5 26 26
FIH (dimer) -0.003 0.028 -10000 0 -10000 0 0
APEX1 -0.008 0.031 -10000 0 -10000 0 0
SERPINE1 -0.082 0.16 -10000 0 -0.41 51 51
FLT1 -0.044 0.19 -10000 0 -0.71 32 32
ADORA2A -0.065 0.17 0.3 29 -0.39 50 79
germ cell development -0.08 0.16 -10000 0 -0.41 52 52
SLC11A2 -0.08 0.16 -10000 0 -0.4 49 49
BHLHE40 -0.08 0.16 -10000 0 -0.4 50 50
HIF1AN -0.003 0.028 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 -0.036 0.11 -10000 0 -0.31 14 14
ETS1 0.021 0.032 -10000 0 -0.36 1 1
CITED2 -0.033 0.19 -10000 0 -0.89 23 23
KDR -0.072 0.27 -10000 0 -0.91 46 46
PGK1 -0.08 0.16 -10000 0 -0.4 50 50
SIRT1 0.02 0.024 -10000 0 -0.35 2 2
response to hypoxia 0 0.001 -10000 0 -10000 0 0
HIF2A/ARNT -0.077 0.19 -10000 0 -0.45 50 50
EPAS1 -0.032 0.071 -10000 0 -0.27 11 11
SP1 0.025 0.007 -10000 0 -10000 0 0
ABCG2 -0.16 0.24 -10000 0 -0.44 203 203
EFNA1 -0.076 0.16 0.35 1 -0.4 50 51
FXN -0.064 0.18 0.3 30 -0.39 48 78
POU5F1 -0.082 0.17 -10000 0 -0.43 52 52
neuron apoptosis 0.076 0.18 0.44 50 -10000 0 50
EP300 0.021 0.006 -10000 0 -10000 0 0
EGLN3 -0.003 0.038 0.28 3 -0.37 1 4
EGLN2 -0.004 0.028 -10000 0 -10000 0 0
EGLN1 -0.002 0.025 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C 0.04 0.02 -10000 0 -0.21 1 1
VHL 0.022 0.017 -10000 0 -0.35 1 1
ARNT -0.005 0.027 -10000 0 -10000 0 0
SLC2A1 -0.063 0.18 0.3 29 -0.39 48 77
TWIST1 -0.085 0.21 0.3 30 -0.5 60 90
ELK1 0.021 0.022 -10000 0 -10000 0 0
HIF2A/ARNT/Cbp/p300 -0.033 0.11 -10000 0 -0.31 9 9
VEGFA -0.08 0.16 -10000 0 -0.4 49 49
CREBBP 0.022 0.005 -10000 0 -10000 0 0
EGFR-dependent Endothelin signaling events

Figure S54.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S54.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HRAS 0.022 0.005 -10000 0 -10000 0 0
EGFR 0.014 0.06 0.33 1 -0.35 13 14
EGF/EGFR -0.02 0.11 0.18 1 -0.18 146 147
EGF/EGFR dimer/SHC/GRB2/SOS1 0.047 0.052 0.23 1 -0.18 10 11
mol:GTP 0 0 -10000 0 -10000 0 0
EDNRA -0.083 0.17 -10000 0 -0.35 146 146
response to oxidative stress 0 0 -10000 0 -10000 0 0
EGF 0.031 0.052 0.28 20 -0.35 1 21
EGF/EGFR dimer/SHC 0.036 0.05 0.2 17 -0.21 10 27
mol:GDP 0.042 0.048 0.21 1 -0.18 10 11
mol:Ca2+ 0 0 -10000 0 -10000 0 0
EDN1 0.018 0.043 -10000 0 -0.35 7 7
GRB2/SOS1 0.031 0.01 -10000 0 -10000 0 0
HRAS/GTP 0.028 0.038 -10000 0 -0.17 10 10
SHC1 0.019 0.009 -10000 0 -10000 0 0
HRAS/GDP 0.04 0.046 -10000 0 -0.17 10 10
FRAP1 -0.013 0.031 0.17 6 -0.17 10 16
EGF/EGFR dimer 0.032 0.057 0.21 20 -0.24 13 33
SOS1 0.023 0.003 -10000 0 -10000 0 0
GRB2 0.022 0.006 -10000 0 -10000 0 0
ETA receptor/Endothelin-1 -0.049 0.13 -10000 0 -0.25 148 148
FAS signaling pathway (CD95)

Figure S55.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S55.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPTAN1 0.006 0.044 0.16 35 -0.18 1 36
RFC1 0.006 0.045 0.16 37 -0.18 2 39
PRKDC 0.019 0.069 0.2 64 -0.18 2 66
RIPK1 0.022 0.007 -10000 0 -10000 0 0
CASP7 -0.001 0.092 -10000 0 -0.56 13 13
FASLG/FAS/FADD/FAF1 0.018 0.053 0.17 37 -0.23 3 40
MAP2K4 0.019 0.094 0.29 6 -0.32 18 24
mol:ceramide 0.012 0.049 0.19 1 -0.23 3 4
GSN 0.005 0.046 0.16 35 -0.18 4 39
FASLG/FAS/FADD/FAF1/Caspase 8 0.02 0.055 0.24 4 -0.21 1 5
FAS 0.018 0.034 -10000 0 -0.35 4 4
BID -0.015 0.019 0.24 2 -0.16 1 3
MAP3K1 0.016 0.091 0.27 6 -0.38 14 20
MAP3K7 0.022 0.007 -10000 0 -10000 0 0
RB1 0.006 0.045 0.17 36 -0.18 1 37
CFLAR 0.022 0.006 -10000 0 -10000 0 0
HGF/MET -0.031 0.13 0.2 3 -0.23 142 145
ARHGDIB 0.007 0.047 0.17 37 -0.18 2 39
FADD 0.021 0.01 -10000 0 -10000 0 0
actin filament polymerization -0.001 0.053 0.19 3 -0.16 34 37
NFKB1 -0.003 0.11 -10000 0 -0.58 16 16
MAPK8 0.013 0.12 0.32 9 -0.44 20 29
DFFA 0.008 0.049 0.17 39 -0.18 1 40
DNA fragmentation during apoptosis 0.003 0.055 0.17 39 -0.18 14 53
FAS/FADD/MET 0.038 0.039 0.2 4 -0.21 8 12
CFLAR/RIP1 0.032 0.01 -10000 0 -10000 0 0
FAIM3 0.019 0.027 0.28 1 -0.35 2 3
FAF1 0.022 0.01 -10000 0 -10000 0 0
PARP1 0.007 0.048 0.17 40 -0.18 2 42
DFFB 0.007 0.047 0.17 39 -0.18 1 40
CHUK -0.008 0.1 0.31 1 -0.54 16 17
FASLG 0.021 0.042 0.29 8 -0.35 2 10
FAS/FADD 0.028 0.028 -10000 0 -0.24 4 4
HGF -0.048 0.14 -10000 0 -0.35 98 98
LMNA 0.012 0.068 0.23 27 -10000 0 27
CASP6 0.007 0.048 0.17 37 -0.18 2 39
CASP10 0.02 0.025 -10000 0 -0.35 2 2
CASP3 0.012 0.052 0.2 36 -10000 0 36
PTPN13 -0.023 0.12 -10000 0 -0.35 63 63
CASP8 -0.016 0.022 0.3 2 -0.19 1 3
IL6 -0.013 0.22 -10000 0 -0.89 26 26
MET 0.021 0.04 0.28 4 -0.35 4 8
ICAD/CAD 0.005 0.048 0.26 6 -10000 0 6
FASLG/FAS/FADD/FAF1/Caspase 10 0.012 0.05 0.19 1 -0.23 3 4
activation of caspase activity by cytochrome c -0.015 0.019 0.24 2 -0.16 1 3
PAK2 0.022 0.077 0.21 68 -0.18 2 70
BCL2 -0.01 0.1 -10000 0 -0.35 44 44
Insulin Pathway

Figure S56.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S56.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CBL/APS/CAP -0.042 0.12 -10000 0 -0.2 170 170
TC10/GTP -0.026 0.094 -10000 0 -0.17 153 153
Insulin Receptor/Insulin/IRS1/Shp2 0.028 0.075 -10000 0 -0.19 50 50
HRAS 0.022 0.005 -10000 0 -10000 0 0
APS homodimer 0.022 0.005 -10000 0 -10000 0 0
GRB14 0.11 0.13 0.28 186 -0.35 2 188
FOXO3 0.017 0.063 -10000 0 -0.58 5 5
AKT1 -0.006 0.08 0.21 28 -0.3 2 30
INSR 0.023 0.008 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.045 0.032 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
GRB10 0.022 0.017 -10000 0 -0.35 1 1
SORBS1 -0.097 0.17 -10000 0 -0.35 166 166
CRK 0.021 0.006 -10000 0 -10000 0 0
PTPN1 -0.004 0.027 0.15 15 -10000 0 15
CAV1 -0.051 0.088 0.16 5 -0.21 106 111
CBL/APS/CAP/Crk-II/C3G -0.018 0.11 -10000 0 -0.18 157 157
Insulin Receptor/Insulin/IRS1/NCK2 0.028 0.075 -10000 0 -0.19 50 50
mol:GDP 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.018 0.064 -10000 0 -0.18 43 43
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B -0.008 0.089 -10000 0 -0.32 26 26
RPS6KB1 -0.012 0.072 0.18 34 -0.28 2 36
PARD6A 0.02 0.007 -10000 0 -10000 0 0
CBL 0.022 0.005 -10000 0 -10000 0 0
tumor necrosis factor-mediated signaling pathway 0 0 -10000 0 -10000 0 0
DOK1 0.014 0.027 -10000 0 -0.57 1 1
PIK3R1 0.018 0.037 -10000 0 -0.35 5 5
Insulin Receptor/Insuli/IRS1/GRB2/Shc -0.007 0.064 0.17 2 -0.29 2 4
HRAS/GTP -0.026 0.038 -10000 0 -0.17 28 28
Insulin Receptor 0.023 0.008 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC 0.032 0.064 -10000 0 -0.18 33 33
PRKCI 0.006 0.067 -10000 0 -0.29 13 13
Insulin Receptor/Insulin/GRB14/PDK1 0.021 0.065 -10000 0 -0.17 41 41
SHC1 0.019 0.009 -10000 0 -10000 0 0
negative regulation of MAPKKK cascade 0.033 0.042 -10000 0 -0.35 4 4
PI3K 0.025 0.068 -10000 0 -0.18 43 43
NCK2 0.023 0.003 -10000 0 -10000 0 0
RHOQ 0.023 0.003 -10000 0 -10000 0 0
mol:H2O2 0 0.004 -10000 0 -10000 0 0
HRAS/GDP 0.016 0.004 -10000 0 -10000 0 0
AKT2 -0.008 0.078 0.23 16 -0.3 2 18
PRKCZ 0.003 0.076 -10000 0 -0.3 16 16
SH2B2 0.022 0.005 -10000 0 -10000 0 0
SHC/SHIP 0.006 0.051 -10000 0 -0.17 33 33
F2RL2 0.002 0.089 0.28 3 -0.35 30 33
TRIP10 0.021 0.006 -10000 0 -10000 0 0
Insulin Receptor/Insulin/Shc 0.032 0.021 -10000 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0.029 0.009 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0.047 0.032 -10000 0 -10000 0 0
RAPGEF1 0.022 0.006 -10000 0 -10000 0 0
RASA1 0.019 0.037 -10000 0 -0.35 5 5
NCK1 0.021 0.023 -10000 0 -0.35 2 2
CBL/APS/CAP/Crk-II -0.025 0.11 -10000 0 -0.19 160 160
TC10/GDP 0.017 0.002 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 0.042 0.029 -10000 0 -0.2 1 1
INPP5D -0.027 0.053 0.15 4 -0.18 50 54
SOS1 0.023 0.003 -10000 0 -10000 0 0
SGK1 0.005 0.069 -10000 0 -0.69 5 5
mol:cAMP 0 0 -10000 0 -10000 0 0
PTPN11 0.023 0.003 -10000 0 -10000 0 0
IRS1 -0.013 0.11 -10000 0 -0.35 50 50
p62DOK/RasGAP 0.034 0.042 -10000 0 -0.36 4 4
INS 0.018 0.009 -10000 0 -10000 0 0
mol:PI-3-4-P2 -0.027 0.052 0.15 4 -0.18 50 54
GRB2 0.022 0.006 -10000 0 -10000 0 0
EIF4EBP1 -0.011 0.075 0.22 27 -0.28 2 29
PTPRA 0.024 0.006 -10000 0 -10000 0 0
PIK3CA 0.02 0.018 -10000 0 -0.35 1 1
TC10/GTP/CIP4 0.029 0.009 -10000 0 -10000 0 0
PDPK1 0.022 0.005 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos -0.001 0.057 -10000 0 -0.19 40 40
Insulin Receptor/Insulin/IRS1 0.017 0.069 -10000 0 -0.19 50 50
Insulin Receptor/Insulin/IRS3 0.03 0.013 -10000 0 -10000 0 0
Par3/Par6 0.034 0.055 0.19 3 -0.18 28 31
RXR and RAR heterodimerization with other nuclear receptor

Figure S57.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S57.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.005 0.073 0.66 2 -0.62 1 3
VDR 0.029 0.044 0.3 13 -10000 0 13
FAM120B 0.022 0.004 -10000 0 -10000 0 0
RXRs/LXRs/DNA/9cRA 0.014 0.076 0.21 11 -0.3 5 16
RXRs/LXRs/DNA/Oxysterols 0.03 0.085 0.29 2 -0.36 6 8
MED1 0.021 0.006 -10000 0 -10000 0 0
mol:9cRA 0.005 0.008 -10000 0 -10000 0 0
RARs/THRs/DNA/Src-1 -0.039 0.1 -10000 0 -0.2 119 119
RXRs/NUR77 0.017 0.1 0.25 5 -0.19 78 83
RXRs/PPAR -0.014 0.087 0.18 5 -0.19 85 90
NCOR2 0.023 0.004 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.019 0.022 0.19 8 -10000 0 8
RARs/VDR/DNA/Vit D3 0.047 0.039 0.22 3 -0.18 8 11
RARA 0.022 0.006 -10000 0 -10000 0 0
NCOA1 0.022 0.017 -10000 0 -0.35 1 1
VDR/VDR/DNA 0.029 0.043 0.3 13 -10000 0 13
RARs/RARs/DNA/9cRA 0.036 0.032 -10000 0 -0.17 9 9
RARG 0.023 0.003 -10000 0 -10000 0 0
RPS6KB1 0.012 0.083 0.57 11 -10000 0 11
RARs/THRs/DNA/SMRT -0.038 0.1 -10000 0 -0.2 122 122
THRA 0.016 0.046 -10000 0 -0.35 8 8
mol:Bile acids 0 0 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.019 0.022 0.19 8 -10000 0 8
RXRs/PPAR/9cRA/PGJ2/DNA 0.025 0.081 0.28 5 -0.18 38 43
NR1H4 0.028 0.049 0.28 19 -10000 0 19
RXRs/LXRs/DNA 0.042 0.087 0.34 1 -0.26 2 3
NR1H2 0.027 0.009 -10000 0 -10000 0 0
NR1H3 0.028 0.015 0.28 1 -10000 0 1
RXRs/VDR/DNA/Vit D3 0.03 0.078 0.23 9 -0.16 52 61
NR4A1 -0.001 0.091 -10000 0 -0.35 33 33
mol:ATRA 0 0 -10000 0 -10000 0 0
RXRs/FXR/9cRA/MED1 0 0.073 0.21 5 -0.18 43 48
RXRG -0.013 0.12 0.31 9 -0.34 57 66
RXR alpha/CCPG 0.034 0.013 -10000 0 -10000 0 0
RXRA 0.026 0.011 -10000 0 -10000 0 0
RXRB 0.028 0.01 -10000 0 -10000 0 0
THRB -0.055 0.15 -10000 0 -0.35 108 108
PPARG 0.004 0.084 0.33 1 -0.35 27 28
PPARD 0.023 0.003 -10000 0 -10000 0 0
TNF 0.03 0.11 0.4 3 -0.76 3 6
mol:Oxysterols 0.005 0.007 -10000 0 -10000 0 0
cholesterol transport 0.03 0.085 0.29 2 -0.35 6 8
PPARA 0.021 0.007 -10000 0 -10000 0 0
mol:Vit D3 0 0 -10000 0 -10000 0 0
RARB 0.016 0.049 -10000 0 -0.35 9 9
RXRs/NUR77/BCL2 -0.033 0.11 0.17 2 -0.25 94 96
SREBF1 0.023 0.077 -10000 0 -0.44 2 2
RXRs/RXRs/DNA/9cRA 0.025 0.081 0.28 5 -0.18 38 43
ABCA1 0.026 0.073 -10000 0 -0.5 1 1
RARs/THRs 0.002 0.11 -10000 0 -0.19 119 119
RXRs/FXR 0.03 0.086 0.25 6 -0.18 56 62
BCL2 -0.01 0.1 -10000 0 -0.35 44 44
Glypican 2 network

Figure S58.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S58.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MDK 0.023 0.014 0.33 1 -9999 0 1
GPC2 0.041 0.068 0.28 37 -9999 0 37
GPC2/Midkine 0.043 0.045 0.21 32 -9999 0 32
neuron projection morphogenesis 0.043 0.045 0.21 32 -9999 0 32
TCGA08_rtk_signaling

Figure S59.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S59.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA -0.076 0.16 -10000 0 -0.35 137 137
HRAS 0.022 0.005 -10000 0 -10000 0 0
EGFR 0.014 0.06 0.33 1 -0.35 13 14
AKT -0.042 0.13 0.29 4 -0.25 120 124
FOXO3 0.023 0.003 -10000 0 -10000 0 0
AKT1 0.022 0.004 -10000 0 -10000 0 0
FOXO1 0.02 0.024 -10000 0 -0.35 2 2
AKT3 -0.096 0.17 -10000 0 -0.35 161 161
FOXO4 0.022 0.023 -10000 0 -0.35 2 2
MET 0.021 0.04 0.28 4 -0.35 4 8
PIK3CA 0.02 0.018 -10000 0 -0.35 1 1
PIK3CB 0.022 0.005 -10000 0 -10000 0 0
NRAS 0.023 0.001 -10000 0 -10000 0 0
PIK3CG 0.013 0.063 0.28 2 -0.35 14 16
PIK3R3 0.023 0.012 0.28 1 -10000 0 1
PIK3R2 0.022 0.005 -10000 0 -10000 0 0
NF1 0.021 0.006 -10000 0 -10000 0 0
RAS -0.011 0.067 0.16 10 -0.13 103 113
ERBB2 0.029 0.05 0.33 14 -10000 0 14
proliferation/survival/translation 0.004 0.089 0.28 13 -0.28 5 18
PI3K 0.003 0.071 0.21 20 -0.22 9 29
PIK3R1 0.018 0.037 -10000 0 -0.35 5 5
KRAS 0.023 0.014 0.33 1 -10000 0 1
FOXO 0.032 0.048 0.23 8 -10000 0 8
AKT2 0.022 0.005 -10000 0 -10000 0 0
PTEN 0.021 0.006 -10000 0 -10000 0 0
Coregulation of Androgen receptor activity

Figure S60.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S60.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NRIP1 0.021 0.029 -10000 0 -0.35 3 3
SVIL -0.017 0.11 -10000 0 -0.35 55 55
ZNF318 0.02 0.011 -10000 0 -10000 0 0
JMJD2C -0.003 0.03 0.084 7 -0.13 26 33
T-DHT/AR/Ubc9 -0.011 0.097 -10000 0 -0.21 89 89
CARM1 0.021 0.006 -10000 0 -10000 0 0
PRDX1 0.023 0.003 -10000 0 -10000 0 0
PELP1 0.021 0.006 -10000 0 -10000 0 0
CTNNB1 0.023 0.005 -10000 0 -10000 0 0
AKT1 0.021 0.009 -10000 0 -10000 0 0
PTK2B 0.02 0.008 -10000 0 -10000 0 0
MED1 0.02 0.009 -10000 0 -10000 0 0
MAK 0.035 0.063 0.28 32 -10000 0 32
response to oxidative stress 0 0.001 -10000 0 -10000 0 0
HIP1 0.02 0.033 -10000 0 -0.35 4 4
GSN 0.019 0.037 -10000 0 -0.35 5 5
NCOA2 0.01 0.064 -10000 0 -0.35 16 16
NCOA6 0.023 0.005 -10000 0 -10000 0 0
DNA-PK 0.036 0.022 -10000 0 -10000 0 0
NCOA4 0.022 0.005 -10000 0 -10000 0 0
PIAS3 0.019 0.009 -10000 0 -10000 0 0
cell proliferation 0.014 0.065 -10000 0 -0.52 2 2
XRCC5 0.021 0.008 -10000 0 -10000 0 0
UBE3A 0.023 0.006 -10000 0 -10000 0 0
T-DHT/AR/SNURF -0.029 0.11 0.19 1 -0.22 121 122
FHL2 -0.006 0.096 -10000 0 -0.85 5 5
RANBP9 0.023 0.005 -10000 0 -10000 0 0
JMJD1A 0.005 0.031 0.095 20 -0.13 18 38
CDK6 0.014 0.056 -10000 0 -0.35 12 12
TGFB1I1 -0.09 0.17 -10000 0 -0.35 158 158
T-DHT/AR/CyclinD1 -0.01 0.097 0.19 1 -0.21 87 88
XRCC6 0.02 0.009 -10000 0 -10000 0 0
T-DHT/AR -0.009 0.12 0.23 1 -0.23 95 96
CTDSP1 0.023 0.004 -10000 0 -10000 0 0
CTDSP2 0.021 0.009 -10000 0 -10000 0 0
BRCA1 0.023 0.006 -10000 0 -10000 0 0
TCF4 0.007 0.07 -10000 0 -0.35 19 19
CDKN2A 0.12 0.13 0.28 207 -10000 0 207
SRF 0.023 0.016 -10000 0 -0.16 2 2
NKX3-1 -0.037 0.16 -10000 0 -0.58 33 33
KLK3 -0.013 0.059 -10000 0 -10000 0 0
TMF1 0.022 0.005 -10000 0 -10000 0 0
HNRNPA1 0.021 0.008 -10000 0 -10000 0 0
AOF2 0.001 0.003 -10000 0 -10000 0 0
APPL1 -0.012 0.004 -10000 0 -10000 0 0
T-DHT/AR/Caspase 8 -0.011 0.097 -10000 0 -0.21 87 87
AR -0.043 0.14 -10000 0 -0.36 87 87
UBA3 0.022 0.005 -10000 0 -10000 0 0
PATZ1 0.02 0.009 -10000 0 -10000 0 0
PAWR 0.023 0.002 -10000 0 -10000 0 0
PRKDC 0.019 0.01 -10000 0 -10000 0 0
PA2G4 0.02 0.009 -10000 0 -10000 0 0
UBE2I 0.022 0.005 -10000 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 -0.008 0.088 -10000 0 -0.19 85 85
RPS6KA3 0.023 0.017 -10000 0 -0.35 1 1
T-DHT/AR/ARA70 -0.011 0.097 -10000 0 -0.22 87 87
LATS2 0.019 0.024 -10000 0 -0.35 2 2
T-DHT/AR/PRX1 -0.008 0.088 -10000 0 -0.19 87 87
Cyclin D3/CDK11 p58 0.017 0.003 -10000 0 -10000 0 0
VAV3 0.085 0.11 0.28 124 -10000 0 124
KLK2 -0.044 0.18 -10000 0 -0.74 30 30
CASP8 0.023 0.003 -10000 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 0 0.096 -10000 0 -0.2 80 80
TMPRSS2 -0.014 0.13 0.29 3 -0.62 15 18
CCND1 0.024 0.018 0.3 2 -10000 0 2
PIAS1 0.023 0.006 -10000 0 -10000 0 0
mol:T-DHT -0.002 0.017 0.039 1 -0.061 33 34
CDC2L1 0 0 -10000 0 -10000 0 0
PIAS4 0.023 0.008 -10000 0 -10000 0 0
T-DHT/AR/CDK6 -0.014 0.1 -10000 0 -0.22 94 94
CMTM2 0.021 0.021 0.28 3 -10000 0 3
SNURF -0.006 0.096 0.28 1 -0.35 37 38
ZMIZ1 0.015 0.039 -10000 0 -0.27 5 5
CCND3 0.022 0.004 -10000 0 -10000 0 0
TGIF1 0.02 0.009 -10000 0 -10000 0 0
FKBP4 0.023 0.005 -10000 0 -10000 0 0
Visual signal transduction: Cones

Figure S61.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S61.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Cone Metarhodopsin II/Cone Transducin 0.024 0.055 0.18 2 -0.18 33 35
RGS9BP 0.033 0.057 0.29 23 -10000 0 23
mol:GTP 0 0 -10000 0 -10000 0 0
GRK1 0.018 0.013 0.28 1 -10000 0 1
mol:Na + 0.016 0.046 0.18 2 -0.2 20 22
mol:ADP -0.014 0.009 0.11 2 -10000 0 2
GNAT2 0.023 0.02 0.28 3 -10000 0 3
RGS9-1/Gbeta5/R9AP -0.007 0.11 0.21 14 -0.21 108 122
mol:GDP 0 0 -10000 0 -10000 0 0
PDE6H/GNAT2/GTP 0.027 0.013 0.18 3 -10000 0 3
GRK7 0.02 0.012 0.28 1 -10000 0 1
CNGB3 0.004 0.071 -10000 0 -0.35 20 20
Cone Metarhodopsin II/X-Arrestin 0.014 0.008 0.19 1 -10000 0 1
mol:Ca2+ -0.007 0.063 0.18 37 -0.19 19 56
Cone PDE6 0.005 0.1 0.22 5 -0.18 106 111
Cone Metarhodopsin II 0.023 0.012 0.18 2 -10000 0 2
Na + (4 Units) 0.025 0.045 0.19 2 -0.19 20 22
GNAT2/GDP 0.003 0.097 0.2 12 -0.18 108 120
GNB5 0.022 0.005 -10000 0 -10000 0 0
mol:GMP (4 units) -0.012 0.025 0.18 8 -10000 0 8
Cone Transducin 0.026 0.059 0.19 2 -0.19 33 35
SLC24A2 0.019 0.014 0.33 1 -10000 0 1
GNB3/GNGT2 0.013 0.07 -10000 0 -0.25 33 33
GNB3 -0.001 0.089 -10000 0 -0.35 32 32
GNAT2/GTP 0.017 0.013 0.19 3 -10000 0 3
CNGA3 0.022 0.02 0.28 3 -10000 0 3
ARR3 0.019 0.012 0.28 1 -10000 0 1
absorption of light 0 0 -10000 0 -10000 0 0
cGMP/Cone CNG Channel 0.016 0.046 0.19 2 -0.2 20 22
mol:Pi -0.008 0.11 0.21 14 -0.21 108 122
Cone CNG Channel 0.033 0.048 -10000 0 -0.18 20 20
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
mol:K + 0.019 0.014 0.33 1 -10000 0 1
RGS9 -0.057 0.15 -10000 0 -0.35 110 110
PDE6C 0.018 0.015 0.33 1 -10000 0 1
GNGT2 0.02 0.029 -10000 0 -0.35 3 3
mol:cGMP (4 units) 0 0 -10000 0 -10000 0 0
PDE6H 0.017 0.004 -10000 0 -10000 0 0
Syndecan-2-mediated signaling events

Figure S62.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S62.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Syndecan-2/Fibronectin 0.014 0.036 -10000 0 -0.2 14 14
EPHB2 0.024 0.02 0.28 3 -10000 0 3
Syndecan-2/TACI 0.018 0.043 0.2 14 -0.19 11 25
LAMA1 0.1 0.13 0.28 166 -0.35 4 170
Syndecan-2/alpha2 ITGB1 0.029 0.055 -10000 0 -0.19 26 26
HRAS 0.022 0.005 -10000 0 -10000 0 0
Syndecan-2/CASK 0.001 0.029 -10000 0 -0.2 11 11
ITGA5 0.023 0.003 -10000 0 -10000 0 0
BAX -0.01 0.028 -10000 0 -10000 0 0
EPB41 0.022 0.017 -10000 0 -0.35 1 1
positive regulation of cell-cell adhesion 0.014 0.029 -10000 0 -0.18 11 11
LAMA3 0.014 0.056 -10000 0 -0.35 12 12
EZR 0.022 0.004 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
CAV2 -0.009 0.1 -10000 0 -0.35 44 44
Syndecan-2/MMP2 0.008 0.051 -10000 0 -0.21 24 24
RP11-540L11.1 0 0 -10000 0 -10000 0 0
alpha2 ITGB1 0.027 0.039 -10000 0 -0.24 10 10
dendrite morphogenesis 0.017 0.038 0.28 3 -0.2 11 14
Syndecan-2/GM-CSF 0.016 0.038 0.2 7 -0.2 11 18
determination of left/right symmetry 0.002 0.035 -10000 0 -0.24 11 11
Syndecan-2/PKC delta 0.015 0.033 -10000 0 -0.2 11 11
GNB2L1 0.022 0.004 -10000 0 -10000 0 0
MAPK3 0.004 0.061 0.19 44 -0.18 10 54
MAPK1 0.003 0.06 0.19 41 -0.18 11 52
Syndecan-2/RACK1 0.025 0.032 -10000 0 -0.17 11 11
NF1 0.021 0.006 -10000 0 -10000 0 0
FGFR/FGF/Syndecan-2 0.002 0.035 -10000 0 -0.24 11 11
ITGA2 0.015 0.051 -10000 0 -0.35 10 10
MAPK8 -0.008 0.032 -10000 0 -0.2 14 14
Syndecan-2/alpha2/beta1 Integrin 0.078 0.095 0.21 143 -0.17 22 165
Syndecan-2/Kininogen 0.022 0.051 0.21 23 -0.2 8 31
ITGB1 0.022 0.004 -10000 0 -10000 0 0
SRC 0.002 0.059 0.18 44 -0.17 11 55
Syndecan-2/CASK/Protein 4.1 0.014 0.031 -10000 0 -0.18 12 12
extracellular matrix organization 0.015 0.034 -10000 0 -0.2 12 12
actin cytoskeleton reorganization 0.014 0.036 -10000 0 -0.2 14 14
Syndecan-2/Caveolin-2/Ras 0.013 0.062 -10000 0 -0.19 41 41
Syndecan-2/Laminin alpha3 0.011 0.046 -10000 0 -0.21 21 21
Syndecan-2/RasGAP 0.032 0.04 -10000 0 -0.17 16 16
alpha5/beta1 Integrin 0.033 0.007 -10000 0 -10000 0 0
PRKCD 0.022 0.005 -10000 0 -10000 0 0
Syndecan-2 dimer 0.017 0.039 0.28 3 -0.2 11 14
GO:0007205 0.001 0 -10000 0 -10000 0 0
DNA mediated transformation 0 0 -10000 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.018 0.037 0.17 4 -0.17 16 20
RHOA 0.022 0.005 -10000 0 -10000 0 0
SDCBP 0.021 0.007 -10000 0 -10000 0 0
TNFRSF13B 0.027 0.044 0.28 15 -10000 0 15
RASA1 0.019 0.037 -10000 0 -0.35 5 5
alpha2/beta1 Integrin 0.027 0.039 -10000 0 -0.24 10 10
Syndecan-2/Synbindin 0.015 0.031 -10000 0 -0.2 10 10
TGFB1 0.022 0.017 -10000 0 -0.35 1 1
CASP3 0.004 0.061 0.19 43 -0.18 11 54
FN1 0.019 0.036 -10000 0 -0.35 5 5
Syndecan-2/IL8 0.068 0.094 0.2 148 -0.2 11 159
SDC2 0.002 0.035 -10000 0 -0.24 11 11
KNG1 0.031 0.058 0.29 24 -10000 0 24
Syndecan-2/Neurofibromin 0.015 0.032 -10000 0 -0.2 11 11
TRAPPC4 0.022 0.005 -10000 0 -10000 0 0
CSF2 0.024 0.032 0.28 8 -10000 0 8
Syndecan-2/TGFB1 0.015 0.034 -10000 0 -0.2 12 12
Syndecan-2/Syntenin/PI-4-5-P2 0.014 0.029 -10000 0 -0.18 11 11
Syndecan-2/Ezrin 0.026 0.033 -10000 0 -0.18 11 11
PRKACA 0.002 0.056 0.19 36 -0.18 10 46
angiogenesis 0.067 0.093 0.2 148 -0.2 11 159
MMP2 0.006 0.072 -10000 0 -0.35 20 20
IL8 0.097 0.12 0.28 150 -10000 0 150
calcineurin-NFAT signaling pathway 0.018 0.043 0.2 14 -0.19 11 25
Presenilin action in Notch and Wnt signaling

Figure S63.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S63.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Delta 1/NOTCH/NOTCH(cleaved) -0.008 0.12 -10000 0 -0.41 38 38
HDAC1 0.021 0.007 -10000 0 -10000 0 0
AES 0.021 0.006 -10000 0 -10000 0 0
FBXW11 0.022 0.004 -10000 0 -10000 0 0
DTX1 0.018 0.04 -10000 0 -0.35 6 6
LRP6/FZD1 0.031 0.022 -10000 0 -0.24 3 3
TLE1 0.022 0.006 -10000 0 -10000 0 0
AP1 -0.047 0.11 -10000 0 -0.22 127 127
NCSTN 0.019 0.009 -10000 0 -10000 0 0
ADAM10 0.02 0.029 -10000 0 -0.35 3 3
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 -0.006 0.15 -10000 0 -0.68 23 23
NICD/RBPSUH -0.005 0.12 -10000 0 -0.4 37 37
WIF1 0.061 0.15 0.28 124 -0.35 32 156
NOTCH1 -0.007 0.099 -10000 0 -0.42 28 28
PSENEN 0.022 0.005 -10000 0 -10000 0 0
KREMEN2 0.045 0.074 0.28 46 -10000 0 46
DKK1 0.069 0.11 0.28 104 -0.35 6 110
beta catenin/beta TrCP1 0.029 0.069 0.22 2 -0.41 4 6
APH1B 0.018 0.04 -10000 0 -0.35 6 6
APH1A 0.019 0.009 -10000 0 -10000 0 0
AXIN1 -0.012 0.11 -10000 0 -0.45 21 21
CtBP/CBP/TCF1/TLE1/AES 0.011 0.038 -10000 0 -0.2 1 1
PSEN1 0.022 0.004 -10000 0 -10000 0 0
FOS -0.087 0.17 -10000 0 -0.35 152 152
JUN 0.018 0.043 -10000 0 -0.35 7 7
MAP3K7 0.022 0.004 -10000 0 -10000 0 0
CTNNB1 0.018 0.07 0.22 3 -0.37 6 9
MAPK3 0.022 0.005 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.041 0.078 0.21 42 -0.2 30 72
HNF1A 0.026 0.032 0.28 8 -10000 0 8
CTBP1 0.022 0.005 -10000 0 -10000 0 0
MYC -0.006 0.17 -10000 0 -1.2 11 11
NKD1 0.033 0.081 0.28 36 -0.35 8 44
FZD1 0.02 0.028 -10000 0 -0.35 3 3
NOTCH1 precursor/Deltex homolog 1 -0.006 0.12 -10000 0 -0.4 35 35
apoptosis -0.047 0.11 -10000 0 -0.22 127 127
Delta 1/NOTCHprecursor -0.009 0.12 -10000 0 -0.41 38 38
DLL1 0.01 0.066 -10000 0 -0.35 17 17
PPARD 0.017 0.058 -10000 0 -0.88 2 2
Gamma Secretase 0.045 0.04 -10000 0 -0.18 6 6
APC -0.011 0.11 -10000 0 -0.53 17 17
DVL1 0.012 0.033 -10000 0 -0.43 2 2
CSNK2A1 0.022 0.004 -10000 0 -10000 0 0
MAP3K7IP1 -0.001 0.002 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 0.083 0.083 0.21 138 -0.2 6 144
LRP6 0.023 0.003 -10000 0 -10000 0 0
CSNK1A1 0.023 0.004 -10000 0 -10000 0 0
NLK 0.009 0.006 -10000 0 -10000 0 0
CCND1 0.008 0.11 -10000 0 -0.85 8 8
WNT1 0.025 0.03 0.28 7 -10000 0 7
Axin1/APC/beta catenin 0.016 0.12 0.25 3 -0.44 20 23
DKK2 0.001 0.088 0.28 2 -0.35 30 32
NOTCH1 precursor/DVL1 -0.012 0.13 -10000 0 -0.51 24 24
GSK3B 0.022 0.004 -10000 0 -10000 0 0
FRAT1 0.022 0.005 -10000 0 -10000 0 0
NOTCH/Deltex homolog 1 -0.005 0.12 -10000 0 -0.4 35 35
PPP2R5D 0.014 0.033 0.22 4 -0.27 3 7
MAPK1 0.022 0.005 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 0.076 0.097 0.36 3 -0.19 33 36
RBPJ 0.022 0.004 -10000 0 -10000 0 0
CREBBP 0.023 0.007 -10000 0 -10000 0 0
TCR signaling in naïve CD8+ T cells

Figure S64.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S64.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GRB2/SOS1/SHC 0.059 0.13 0.28 82 -0.35 17 99
FYN 0.032 0.13 0.28 28 -0.41 19 47
LAT/GRAP2/SLP76 0.033 0.11 0.28 13 -0.37 21 34
IKBKB 0.021 0.007 -10000 0 -10000 0 0
AKT1 0.022 0.11 0.27 20 -0.31 27 47
B2M 0.023 0.008 -10000 0 -10000 0 0
IKBKG 0.01 0.037 0.13 12 -0.11 14 26
MAP3K8 0.02 0.029 -10000 0 -0.35 3 3
mol:Ca2+ -0.012 0.012 0.086 1 -0.078 4 5
integrin-mediated signaling pathway 0.026 0.011 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1/PI3K Class IA 0.02 0.14 0.33 15 -0.42 30 45
TRPV6 -0.013 0.18 1.2 9 -10000 0 9
CD28 0.024 0.017 0.28 2 -10000 0 2
SHC1 0.046 0.15 0.3 80 -0.38 24 104
receptor internalization 0.018 0.12 0.31 6 -0.4 29 35
PRF1 0.012 0.17 0.41 5 -0.79 16 21
KRAS 0.023 0.014 0.33 1 -10000 0 1
GRB2 0.022 0.006 -10000 0 -10000 0 0
COT/AKT1 0.03 0.092 0.27 15 -0.26 23 38
LAT 0.022 0.12 0.3 12 -0.39 25 37
EntrezGene:6955 0 0.003 -10000 0 -0.036 1 1
CD3D 0.025 0.062 0.29 14 -0.36 7 21
CD3E 0.019 0.057 0.3 5 -0.36 9 14
CD3G 0.024 0.04 0.29 7 -0.35 2 9
RASGRP2 -0.014 0.059 0.083 3 -0.16 73 76
RASGRP1 0.016 0.12 0.3 18 -0.39 21 39
HLA-A 0.024 0.013 0.28 1 -10000 0 1
RASSF5 0.02 0.008 -10000 0 -10000 0 0
RAP1A/GTP/RAPL 0.026 0.011 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.028 0.069 0.15 79 -0.12 20 99
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.005 0.04 -10000 0 -0.16 22 22
PRKCA 0.009 0.065 0.18 12 -0.22 13 25
GRAP2 0.011 0.062 -10000 0 -0.35 15 15
mol:IP3 0.013 0.086 0.2 34 -0.29 18 52
EntrezGene:6957 0.001 0.003 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 0.009 0.084 0.28 6 -0.42 13 19
ORAI1 -0.001 0.15 0.37 7 -0.98 9 16
CSK 0.022 0.12 0.32 7 -0.4 23 30
B7 family/CD28 0.052 0.12 0.39 12 -0.39 17 29
CHUK 0.022 0.005 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 0.02 0.13 0.32 7 -0.43 26 33
PTPN6 0.021 0.12 0.29 10 -0.38 26 36
VAV1 0.021 0.12 0.31 8 -0.4 24 32
Monovalent TCR/CD3 0.011 0.054 0.23 8 -0.26 13 21
CBL 0.022 0.005 -10000 0 -10000 0 0
LCK 0.03 0.13 0.28 27 -0.43 19 46
PAG1 0.026 0.12 0.3 11 -0.39 23 34
RAP1A 0.023 0.001 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK 0.02 0.13 0.28 11 -0.42 26 37
CD80 0.037 0.06 0.28 29 -10000 0 29
CD86 0.024 0.017 0.29 2 -10000 0 2
PDK1/CARD11/BCL10/MALT1 0.003 0.053 0.18 2 -0.2 22 24
HRAS 0.022 0.005 -10000 0 -10000 0 0
GO:0035030 0.018 0.095 0.28 10 -0.33 18 28
CD8A 0.019 0.055 0.3 4 -0.35 9 13
CD8B 0.031 0.072 0.28 25 -0.36 7 32
PTPRC 0.015 0.045 0.28 1 -0.35 7 8
PDK1/PKC theta 0.018 0.13 0.31 20 -0.39 22 42
CSK/PAG1 0.027 0.12 0.3 15 -0.38 23 38
SOS1 0.023 0.003 -10000 0 -10000 0 0
peptide-MHC class I 0.034 0.014 0.21 1 -10000 0 1
GRAP2/SLP76 0.036 0.13 0.33 8 -0.4 25 33
STIM1 0.002 0.062 1.2 1 -10000 0 1
RAS family/GTP 0.038 0.075 0.19 38 -0.17 14 52
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin 0.017 0.12 0.32 6 -0.42 29 35
mol:DAG -0.005 0.062 -10000 0 -0.25 21 21
RAP1A/GDP 0.016 0.033 0.088 34 -0.063 10 44
PLCG1 0.022 0.005 -10000 0 -10000 0 0
CD247 0.019 0.028 0.3 1 -0.35 2 3
cytotoxic T cell degranulation 0.013 0.16 0.41 5 -0.75 16 21
RAP1A/GTP -0.006 0.022 -10000 0 -0.059 75 75
mol:PI-3-4-5-P3 0.022 0.12 0.3 18 -0.36 29 47
LAT/GRAP2/SLP76/VAV1/PLCgamma1 0.028 0.11 0.28 15 -0.36 19 34
NRAS 0.023 0.001 -10000 0 -10000 0 0
ZAP70 0.03 0.051 0.28 16 -0.35 2 18
GRB2/SOS1 0.031 0.01 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 0.022 0.1 0.33 5 -0.36 20 25
MALT1 0.022 0.005 -10000 0 -10000 0 0
TRAF6 0.022 0.005 -10000 0 -10000 0 0
CD8 heterodimer 0.037 0.071 0.24 26 -0.26 15 41
CARD11 0.027 0.042 0.28 11 -0.35 1 12
PRKCB 0.01 0.071 0.18 13 -0.25 18 31
PRKCE 0.015 0.061 0.18 13 -0.21 12 25
PRKCQ 0.017 0.14 0.32 19 -0.41 27 46
LCP2 0.023 0.012 0.28 1 -10000 0 1
BCL10 0.023 0.002 -10000 0 -10000 0 0
regulation of survival gene product expression 0.023 0.098 0.25 21 -0.27 26 47
IKK complex 0.017 0.06 0.19 28 -0.11 8 36
RAS family/GDP -0.001 0.009 -10000 0 -0.04 3 3
MAP3K14 0.021 0.072 0.22 17 -0.2 21 38
PDPK1 0.022 0.1 0.29 17 -0.3 27 44
TCR/CD3/MHC I/CD8/Fyn 0.01 0.16 0.39 4 -0.49 32 36
Syndecan-4-mediated signaling events

Figure S65.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S65.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0.027 0.075 0.23 1 -0.42 8 9
Syndecan-4/Syndesmos 0.057 0.11 0.37 4 -0.74 2 6
positive regulation of JNK cascade -0.033 0.13 0.44 1 -0.45 8 9
Syndecan-4/ADAM12 0.06 0.11 0.33 7 -0.74 2 9
CCL5 0.021 0.046 0.28 6 -0.35 5 11
Rac1/GDP 0.016 0.003 -10000 0 -10000 0 0
DNM2 0.021 0.007 -10000 0 -10000 0 0
ITGA5 0.023 0.003 -10000 0 -10000 0 0
SDCBP 0.021 0.007 -10000 0 -10000 0 0
PLG -0.006 0.1 0.27 8 -0.33 42 50
ADAM12 0.027 0.036 0.28 10 -10000 0 10
mol:GTP 0 0 -10000 0 -10000 0 0
NUDT16L1 0.022 0.005 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
Syndecan-4/PKC alpha -0.04 0.023 -10000 0 -10000 0 0
Syndecan-4/Laminin alpha1 0.1 0.14 0.37 21 -0.74 2 23
Syndecan-4/CXCL12/CXCR4 -0.034 0.13 0.45 1 -0.48 8 9
Syndecan-4/Laminin alpha3 0.053 0.11 0.35 6 -0.74 2 8
MDK 0.023 0.014 0.33 1 -10000 0 1
Syndecan-4/FZD7 0.041 0.11 0.33 4 -0.74 2 6
Syndecan-4/Midkine 0.057 0.11 0.33 8 -0.74 2 10
FZD7 -0.037 0.14 -10000 0 -0.35 83 83
Syndecan-4/FGFR1/FGF -0.028 0.12 -10000 0 -0.45 7 7
THBS1 -0.023 0.12 -10000 0 -0.35 63 63
integrin-mediated signaling pathway 0.052 0.1 0.31 7 -0.57 3 10
positive regulation of MAPKKK cascade -0.033 0.13 0.44 1 -0.45 8 9
Syndecan-4/TACI 0.057 0.11 0.37 6 -0.74 2 8
CXCR4 0.023 0.002 -10000 0 -10000 0 0
cell adhesion 0.009 0.046 0.18 12 -0.2 6 18
Syndecan-4/Dynamin 0.054 0.1 0.34 6 -0.66 2 8
Syndecan-4/TSP1 0.042 0.12 0.37 3 -0.53 5 8
Syndecan-4/GIPC 0.054 0.1 0.37 3 -0.66 2 5
Syndecan-4/RANTES 0.057 0.11 0.32 8 -0.74 2 10
ITGB1 0.022 0.004 -10000 0 -10000 0 0
LAMA1 0.1 0.13 0.28 166 -0.35 4 170
LAMA3 0.014 0.056 -10000 0 -0.35 12 12
RAC1 0.022 0.005 -10000 0 -10000 0 0
PRKCA -0.015 0.13 0.71 12 -0.33 24 36
Syndecan-4/alpha-Actinin 0.057 0.11 0.34 7 -0.74 2 9
TFPI -0.021 0.12 -10000 0 -0.35 61 61
F2 0.049 0.076 0.29 46 -10000 0 46
alpha5/beta1 Integrin 0.033 0.007 -10000 0 -10000 0 0
positive regulation of cell adhesion 0.064 0.11 0.34 13 -0.71 2 15
ACTN1 0.022 0.004 -10000 0 -10000 0 0
TNC 0.014 0.055 0.28 1 -0.35 11 12
Syndecan-4/CXCL12 -0.017 0.13 0.46 1 -0.42 14 15
FGF6 0.016 0.003 -10000 0 -10000 0 0
RHOA 0.022 0.005 -10000 0 -10000 0 0
CXCL12 -0.2 0.18 -10000 0 -0.35 315 315
TNFRSF13B 0.027 0.044 0.28 15 -10000 0 15
FGF2 -0.17 0.18 -10000 0 -0.35 265 265
FGFR1 0.02 0.018 -10000 0 -0.35 1 1
Syndecan-4/PI-4-5-P2 0.039 0.1 0.29 6 -0.74 2 8
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.016 0.04 -10000 0 -0.33 5 5
cell migration -0.022 0.015 -10000 0 -10000 0 0
PRKCD 0.019 0.018 -10000 0 -0.12 1 1
vasculogenesis 0.041 0.11 0.33 6 -0.51 5 11
SDC4 0.049 0.095 0.31 6 -0.88 1 7
Syndecan-4/Tenascin C 0.053 0.11 0.32 7 -0.6 3 10
Syndecan-4/PI-4-5-P2/PKC alpha -0.033 0.018 -10000 0 -10000 0 0
Syndecan-4/Syntenin 0.054 0.1 0.34 7 -0.74 2 9
MMP9 0.13 0.13 0.28 213 -10000 0 213
Rac1/GTP 0.009 0.046 0.19 12 -0.2 6 18
cytoskeleton organization 0.056 0.1 0.34 7 -0.7 2 9
GIPC1 0.022 0.006 -10000 0 -10000 0 0
Syndecan-4/TFPI 0.043 0.12 0.34 3 -0.63 3 6
Signaling events mediated by PTP1B

Figure S66.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S66.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.009 0.07 -10000 0 -0.35 19 19
Jak2/Leptin Receptor -0.072 0.17 -10000 0 -0.41 70 70
PTP1B/AKT1 -0.003 0.084 0.28 1 -0.28 26 27
FYN 0.022 0.004 -10000 0 -10000 0 0
p210 bcr-abl/PTP1B -0.014 0.088 0.32 1 -0.3 29 30
EGFR 0.013 0.061 0.32 1 -0.36 13 14
EGF/EGFR 0.007 0.091 0.24 4 -0.27 25 29
CSF1 0.016 0.051 -10000 0 -0.35 10 10
AKT1 0.022 0.007 -10000 0 -10000 0 0
INSR 0.021 0.007 -10000 0 -10000 0 0
PTP1B/N-cadherin -0.024 0.1 -10000 0 -0.29 44 44
Insulin Receptor/Insulin 0.01 0.082 0.25 1 -0.29 16 17
HCK 0.025 0.03 0.28 7 -10000 0 7
CRK 0.021 0.006 -10000 0 -10000 0 0
TYK2 -0.005 0.09 0.23 17 -0.28 26 43
EGF 0.03 0.054 0.28 20 -0.34 1 21
YES1 0.022 0.005 -10000 0 -10000 0 0
CAV1 -0.029 0.11 0.27 4 -0.32 38 42
TXN 0.022 0.006 -10000 0 -10000 0 0
PTP1B/IRS1/GRB2 -0.011 0.1 -10000 0 -0.27 44 44
cell migration 0.014 0.088 0.3 29 -0.32 1 30
STAT3 0.022 0.006 -10000 0 -10000 0 0
PRLR -0.049 0.15 -10000 0 -0.35 99 99
ITGA2B 0.018 0.039 0.28 1 -0.35 5 6
CSF1R 0.021 0.031 0.28 1 -0.35 3 4
Prolactin Receptor/Prolactin -0.027 0.12 0.21 3 -0.26 106 109
FGR 0.015 0.051 -10000 0 -0.35 10 10
PTP1B/p130 Cas -0.002 0.085 0.29 1 -0.28 29 30
Crk/p130 Cas 0.005 0.087 0.28 1 -0.29 22 23
DOK1 -0.018 0.097 0.23 4 -0.33 29 33
JAK2 -0.054 0.15 0.29 1 -0.45 38 39
Jak2/Leptin Receptor/Leptin -0.011 0.094 -10000 0 -0.34 19 19
PIK3R1 0.018 0.037 -10000 0 -0.35 5 5
PTPN1 -0.014 0.089 0.32 1 -0.3 29 30
LYN 0.021 0.007 -10000 0 -10000 0 0
CDH2 -0.029 0.13 -10000 0 -0.35 71 71
SRC 0 0.11 -10000 0 -0.52 19 19
ITGB3 -0.038 0.14 0.28 2 -0.35 85 87
CAT1/PTP1B -0.003 0.12 0.28 12 -0.38 22 34
CAPN1 0.022 0.004 -10000 0 -10000 0 0
CSK 0.022 0.005 -10000 0 -10000 0 0
PI3K 0.014 0.078 -10000 0 -0.3 12 12
mol:H2O2 0 0.003 -10000 0 -10000 0 0
STAT3 (dimer) -0.009 0.086 -10000 0 -0.31 18 18
negative regulation of transcription -0.054 0.15 0.29 1 -0.45 38 39
FCGR2A 0.02 0.014 0.28 1 -10000 0 1
FER 0.023 0.004 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin -0.016 0.11 0.21 3 -0.25 90 93
BLK 0.037 0.067 0.28 36 -10000 0 36
Insulin Receptor/Insulin/Shc 0.032 0.019 -10000 0 -10000 0 0
RHOA 0.022 0.005 -10000 0 -10000 0 0
LEPR -0.089 0.17 -10000 0 -0.35 157 157
BCAR1 0.02 0.007 -10000 0 -10000 0 0
p210 bcr-abl/Grb2 0.022 0.006 -10000 0 -10000 0 0
mol:NADPH 0 0.002 -10000 0 -10000 0 0
TRPV6 0.008 0.11 0.28 9 -0.41 17 26
PRL 0.007 0.067 0.28 4 -0.35 15 19
SOCS3 0 0.16 -10000 0 -1.1 11 11
SPRY2 0.019 0.033 -10000 0 -0.36 4 4
Insulin Receptor/Insulin/IRS1 0.014 0.075 -10000 0 -0.21 50 50
CSF1/CSF1R 0.001 0.095 -10000 0 -0.28 32 32
Ras protein signal transduction 0.021 0.12 0.55 25 -10000 0 25
IRS1 -0.013 0.11 -10000 0 -0.35 50 50
INS 0.009 0.015 -10000 0 -10000 0 0
LEP 0.016 0.021 0.28 2 -10000 0 2
STAT5B -0.032 0.12 0.32 1 -0.37 41 42
STAT5A -0.032 0.12 0.32 1 -0.36 42 43
GRB2 0.022 0.006 -10000 0 -10000 0 0
PDGFB-D/PDGFRB -0.01 0.094 -10000 0 -0.29 35 35
CSN2 -0.021 0.078 0.33 1 -0.47 5 6
PIK3CA 0.02 0.018 -10000 0 -0.35 1 1
LAT 0.008 0.093 -10000 0 -0.52 13 13
YBX1 0.026 0.017 -10000 0 -0.35 1 1
LCK 0.024 0.028 0.28 4 -0.35 1 5
SHC1 0.019 0.009 -10000 0 -10000 0 0
NOX4 0.02 0.035 0.28 1 -0.35 4 5
Calcium signaling in the CD4+ TCR pathway

Figure S67.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S67.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC1 0.003 0.037 -10000 0 -0.2 13 13
NFATC2 -0.009 0.061 -10000 0 -0.21 43 43
NFATC3 0.007 0.018 -10000 0 -10000 0 0
CD40LG -0.05 0.14 0.32 1 -0.36 44 45
PTGS2 -0.056 0.16 -10000 0 -0.41 56 56
JUNB 0.018 0.037 -10000 0 -0.35 5 5
CaM/Ca2+/Calcineurin A alpha-beta B1 0.014 0.015 -10000 0 -10000 0 0
CaM/Ca2+ 0.014 0.015 -10000 0 -10000 0 0
CALM1 0.02 0.014 -10000 0 -10000 0 0
JUN 0.015 0.045 -10000 0 -0.35 7 7
mol:Ca2+ 0 0.005 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.014 0.008 -10000 0 -10000 0 0
FOSL1 0.042 0.069 0.28 40 -10000 0 40
CREM 0.021 0.008 -10000 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT 0.008 0.087 0.24 1 -0.28 16 17
FOS -0.088 0.17 -10000 0 -0.35 152 152
IFNG -0.039 0.14 0.26 10 -0.36 30 40
AP-1/NFAT1-c-4 -0.026 0.17 0.35 12 -0.37 45 57
FASLG -0.042 0.12 0.26 5 -0.33 44 49
NFAT1-c-4/ICER1 -0.001 0.073 -10000 0 -0.24 15 15
IL2RA -0.041 0.13 0.27 8 -0.35 30 38
FKBP12/FK506 0.017 0.003 -10000 0 -10000 0 0
CSF2 -0.046 0.13 0.27 4 -0.34 39 43
JunB/Fra1/NFAT1-c-4 0.018 0.09 0.21 27 -0.23 16 43
IL4 -0.048 0.13 0.32 1 -0.36 31 32
IL2 -0.011 0.16 -10000 0 -0.86 18 18
IL3 -0.003 0.1 -10000 0 -0.66 12 12
FKBP1A 0.022 0.004 -10000 0 -10000 0 0
BATF3 0.02 0.014 0.28 1 -10000 0 1
mol:FK506 0 0 -10000 0 -10000 0 0
POU2F1 0.019 0.009 -10000 0 -10000 0 0
Regulation of Androgen receptor activity

Figure S68.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S68.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 -0.01 0.005 -10000 0 -10000 0 0
SMARCC1 0.009 0.015 -10000 0 -10000 0 0
REL 0.021 0.009 -10000 0 -10000 0 0
HDAC7 -0.012 0.062 0.21 8 -0.26 8 16
JUN 0.018 0.043 -10000 0 -0.35 7 7
EP300 0.022 0.006 -10000 0 -10000 0 0
KAT2B 0.017 0.046 -10000 0 -0.35 8 8
KAT5 0.022 0.004 -10000 0 -10000 0 0
MAPK14 0.007 0.045 0.21 6 -10000 0 6
FOXO1 0.02 0.024 -10000 0 -0.35 2 2
T-DHT/AR 0.021 0.076 0.29 4 -0.26 8 12
MAP2K6 0.052 0.087 0.28 63 -10000 0 63
BRM/BAF57 0.025 0.044 -10000 0 -0.24 13 13
MAP2K4 0.018 0.02 -10000 0 -0.34 1 1
SMARCA2 0.012 0.06 -10000 0 -0.35 14 14
PDE9A -0.004 0.1 -10000 0 -0.63 9 9
NCOA2 0.008 0.065 -10000 0 -0.35 16 16
CEBPA 0.021 0.033 0.28 2 -0.35 3 5
EHMT2 0.023 0.004 -10000 0 -10000 0 0
cell proliferation 0.003 0.14 0.35 19 -0.36 26 45
NR0B1 0.033 0.06 0.28 29 -10000 0 29
EGR1 -0.023 0.12 -10000 0 -0.35 65 65
RXRs/9cRA 0.012 0.074 0.21 8 -0.18 56 64
AR/RACK1/Src -0.001 0.073 0.24 6 -0.24 10 16
AR/GR -0.039 0.12 0.21 4 -0.22 126 130
GNB2L1 0.021 0.008 -10000 0 -10000 0 0
PKN1 0.022 0.006 -10000 0 -10000 0 0
RCHY1 0.022 0.004 -10000 0 -10000 0 0
epidermal growth factor receptor activity 0 0.002 -10000 0 -0.012 8 8
MAPK8 -0.009 0.024 -10000 0 -0.25 4 4
T-DHT/AR/TIF2/CARM1 0.008 0.074 0.22 4 -0.26 13 17
SRC -0.003 0.051 0.18 29 -0.18 3 32
NR3C1 -0.033 0.13 -10000 0 -0.35 78 78
KLK3 0.024 0.11 0.38 3 -0.43 3 6
APPBP2 0.022 0.009 -10000 0 -10000 0 0
TRIM24 0.023 0.005 -10000 0 -10000 0 0
T-DHT/AR/TIP60 0.001 0.065 0.21 13 -0.22 6 19
TMPRSS2 -0.007 0.15 0.4 1 -0.77 14 15
RXRG -0.017 0.12 0.31 9 -0.35 57 66
mol:9cRA 0 0 -10000 0 -10000 0 0
RXRA 0.022 0.006 -10000 0 -10000 0 0
RXRB 0.023 0.004 -10000 0 -10000 0 0
CARM1 0.02 0.01 -10000 0 -10000 0 0
NR2C2 0.016 0.049 -10000 0 -0.35 9 9
KLK2 -0.016 0.13 -10000 0 -0.49 27 27
AR -0.02 0.086 0.16 17 -0.22 71 88
SENP1 0.023 0.004 -10000 0 -10000 0 0
HSP90AA1 0.022 0.004 -10000 0 -10000 0 0
MDM2 0.021 0.009 -10000 0 -10000 0 0
SRY -0.001 0.003 -10000 0 -0.016 18 18
GATA2 -0.011 0.11 -10000 0 -0.35 47 47
MYST2 0 0.001 -10000 0 -10000 0 0
HOXB13 0.19 0.12 0.28 340 -10000 0 340
T-DHT/AR/RACK1/Src -0.004 0.071 0.24 10 -0.23 6 16
positive regulation of transcription -0.011 0.11 -10000 0 -0.35 47 47
DNAJA1 0.022 0.009 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.012 0.004 -10000 0 -10000 0 0
NCOA1 0.026 0.023 -10000 0 -0.38 1 1
SPDEF 0.083 0.15 0.28 153 -0.35 23 176
T-DHT/AR/TIF2 -0.002 0.094 0.24 13 -0.32 22 35
T-DHT/AR/Hsp90 0.003 0.066 0.21 14 -0.23 5 19
GSK3B 0.023 0.006 -10000 0 -10000 0 0
NR2C1 0.023 0.002 -10000 0 -10000 0 0
mol:T-DHT -0.008 0.036 0.21 8 -0.19 3 11
SIRT1 0.021 0.023 -10000 0 -0.35 2 2
ZMIZ2 0.02 0.01 -10000 0 -10000 0 0
POU2F1 0.024 0.025 -10000 0 -10000 0 0
T-DHT/AR/DAX-1 0.003 0.076 0.21 27 -0.22 6 33
CREBBP 0.022 0.005 -10000 0 -10000 0 0
SMARCE1 0.022 0.006 -10000 0 -10000 0 0
Signaling events mediated by VEGFR1 and VEGFR2

Figure S69.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S69.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
alphaV beta3 Integrin -0.013 0.1 0.21 2 -0.24 85 87
AKT1 -0.014 0.15 0.34 5 -0.48 35 40
PTK2B -0.054 0.13 -10000 0 -0.5 29 29
VEGFR2 homodimer/Frs2 -0.005 0.13 -10000 0 -0.53 29 29
CAV1 -0.041 0.14 -10000 0 -0.35 88 88
CALM1 0.022 0.004 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 0.01 0.12 -10000 0 -0.48 29 29
endothelial cell proliferation -0.021 0.15 0.34 14 -0.44 42 56
mol:Ca2+ -0.043 0.12 -10000 0 -0.48 30 30
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac 0.02 0.12 -10000 0 -0.46 29 29
RP11-342D11.1 -0.04 0.12 -10000 0 -0.48 30 30
CDH5 0.016 0.04 -10000 0 -0.35 6 6
VEGFA homodimer 0.044 0.029 -10000 0 -0.19 1 1
SHC1 0.019 0.009 -10000 0 -10000 0 0
SHC2 -0.027 0.12 -10000 0 -0.35 67 67
HRAS/GDP -0.002 0.11 -10000 0 -0.43 27 27
SH2D2A 0.029 0.052 0.29 20 -10000 0 20
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS 0.002 0.13 -10000 0 -0.44 34 34
VEGFR2 homodimer/VEGFA homodimer/TsAd 0.01 0.12 -10000 0 -0.47 29 29
VEGFR1 homodimer 0.022 0.005 -10000 0 -10000 0 0
SHC/GRB2/SOS1 0.01 0.12 -10000 0 -0.47 27 27
GRB10 -0.043 0.12 -10000 0 -0.5 29 29
PTPN11 0.023 0.003 -10000 0 -10000 0 0
GRB2 0.022 0.006 -10000 0 -10000 0 0
PAK1 0.022 0.004 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin 0.026 0.13 -10000 0 -0.48 28 28
HRAS 0.022 0.005 -10000 0 -10000 0 0
VEGF/Rho/ROCK1/Integrin Complex -0.029 0.11 -10000 0 -0.35 36 36
HIF1A 0.022 0.004 -10000 0 -10000 0 0
FRS2 0.023 0.003 -10000 0 -10000 0 0
oxygen and reactive oxygen species metabolic process 0.019 0.12 -10000 0 -0.46 29 29
mol:GTP 0 0 -10000 0 -10000 0 0
FLT4 0.009 0.07 -10000 0 -0.35 19 19
Nck/Pak 0.031 0.019 -10000 0 -0.24 2 2
VEGFR2 homodimer/VEGFA homodimer/Fyn 0.009 0.12 -10000 0 -0.48 29 29
mol:GDP 0.003 0.12 -10000 0 -0.44 28 28
mol:NADP -0.008 0.12 0.33 8 -0.38 36 44
eNOS/Hsp90 0.001 0.12 0.35 6 -0.36 36 42
PIK3R1 0.018 0.037 -10000 0 -0.35 5 5
mol:IP3 -0.043 0.12 -10000 0 -0.49 30 30
HIF1A/ARNT 0.026 0.015 -10000 0 -10000 0 0
SHB 0.022 0.004 -10000 0 -10000 0 0
VEGFA 0.023 0.004 -10000 0 -10000 0 0
VEGFC 0.016 0.046 -10000 0 -0.35 8 8
FAK1/Vinculin -0.027 0.15 -10000 0 -0.56 30 30
mol:Ca ++ 0 0 -10000 0 -10000 0 0
RHOA 0.022 0.005 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.013 0.15 -10000 0 -0.51 30 30
PTPN6 0.023 0.014 0.33 1 -10000 0 1
EPAS1 0.008 0.077 -10000 0 -0.31 29 29
mol:L-citrulline -0.008 0.12 0.33 8 -0.38 36 44
ITGAV 0.023 0.003 -10000 0 -10000 0 0
PIK3CA 0.02 0.018 -10000 0 -0.35 1 1
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 0.021 0.11 -10000 0 -0.44 29 29
VEGFR2 homodimer/VEGFA homodimer -0.002 0.14 -10000 0 -0.52 30 30
VEGFR2/3 heterodimer -0.013 0.14 -10000 0 -0.54 29 29
VEGFB 0.022 0.004 -10000 0 -10000 0 0
MAPK11 -0.04 0.13 0.34 2 -0.52 31 33
VEGFR2 homodimer -0.02 0.14 -10000 0 -0.61 28 28
FLT1 0.022 0.005 -10000 0 -10000 0 0
NEDD4 -0.002 0.092 -10000 0 -0.35 34 34
MAPK3 -0.039 0.13 0.3 9 -0.44 34 43
MAPK1 -0.04 0.13 0.3 9 -0.44 34 43
VEGFA145/NRP2 0.021 0.059 -10000 0 -0.24 24 24
VEGFR1/2 heterodimer -0.006 0.13 -10000 0 -0.52 29 29
KDR -0.02 0.14 -10000 0 -0.61 28 28
VEGFA165/NRP1/VEGFR2 homodimer -0.008 0.14 -10000 0 -0.48 33 33
SRC 0.022 0.005 -10000 0 -10000 0 0
platelet activating factor biosynthetic process -0.041 0.13 0.3 9 -0.44 36 45
PI3K -0.016 0.14 -10000 0 -0.53 29 29
VEGFR2 homodimer/VEGFA homodimer/NCK1 0.009 0.12 -10000 0 -0.48 29 29
FES -0.044 0.12 -10000 0 -0.49 31 31
GAB1 -0.003 0.14 -10000 0 -0.54 29 29
VEGFR2 homodimer/VEGFA homodimer/Src 0.009 0.12 -10000 0 -0.48 29 29
CTNNB1 0.022 0.004 -10000 0 -10000 0 0
SOS1 0.023 0.003 -10000 0 -10000 0 0
ARNT 0.018 0.01 -10000 0 -10000 0 0
eNOS/Caveolin-1 -0.019 0.13 0.31 4 -0.41 37 41
VEGFR2 homodimer/VEGFA homodimer/Yes 0.009 0.12 -10000 0 -0.48 29 29
PI3K/GAB1 -0.001 0.14 -10000 0 -0.49 30 30
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak 0.031 0.12 -10000 0 -0.44 29 29
PRKACA 0.022 0.005 -10000 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer -0.003 0.14 -10000 0 -0.51 30 30
HSP90AA1 0.022 0.004 -10000 0 -10000 0 0
CDC42 -0.043 0.12 -10000 0 -0.5 30 30
actin cytoskeleton reorganization 0.01 0.12 -10000 0 -0.47 29 29
PTK2 -0.041 0.15 0.25 3 -0.6 29 32
EDG1 -0.04 0.12 -10000 0 -0.48 30 30
mol:DAG -0.043 0.12 -10000 0 -0.49 30 30
CaM/Ca2+ -0.012 0.12 -10000 0 -0.46 30 30
MAP2K3 -0.04 0.11 -10000 0 -0.47 27 27
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 -0.001 0.14 -10000 0 -0.51 30 30
PLCG1 -0.044 0.12 -10000 0 -0.5 30 30
VEGFR2 homodimer/VEGFA homodimer/Src/Shb 0.02 0.12 -10000 0 -0.46 29 29
IQGAP1 0.022 0.004 -10000 0 -10000 0 0
YES1 0.022 0.005 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP2 0.01 0.12 -10000 0 -0.48 29 29
VEGFR2 homodimer/VEGFA homodimer/SHP1 0.01 0.12 -10000 0 -0.48 29 29
cell migration -0.025 0.14 0.28 1 -0.5 31 32
mol:PI-3-4-5-P3 -0.014 0.13 -10000 0 -0.49 29 29
FYN 0.022 0.004 -10000 0 -10000 0 0
VEGFB/NRP1 -0.018 0.12 -10000 0 -0.46 30 30
mol:NO -0.008 0.12 0.33 8 -0.38 36 44
PXN 0.023 0.003 -10000 0 -10000 0 0
HRAS/GTP -0.013 0.1 -10000 0 -0.43 27 27
VEGFR2 homodimer/VEGFA homodimer/GRB10 -0.009 0.13 -10000 0 -0.51 30 30
VHL 0.022 0.017 -10000 0 -0.35 1 1
ITGB3 -0.038 0.14 0.28 2 -0.35 85 87
NOS3 -0.011 0.14 0.36 6 -0.42 36 42
VEGFR2 homodimer/VEGFA homodimer/Sck -0.02 0.14 -10000 0 -0.49 30 30
RAC1 0.022 0.005 -10000 0 -10000 0 0
PRKCA -0.049 0.12 -10000 0 -0.47 31 31
PRKCB -0.05 0.12 -10000 0 -0.48 31 31
VCL 0.022 0.005 -10000 0 -10000 0 0
VEGFA165/NRP1 -0.016 0.13 -10000 0 -0.48 30 30
VEGFR1/2 heterodimer/VEGFA homodimer 0.009 0.12 -10000 0 -0.48 29 29
VEGFA165/NRP2 0.021 0.059 -10000 0 -0.24 24 24
MAPKKK cascade -0.011 0.13 0.33 3 -0.45 25 28
NRP2 0.006 0.078 -10000 0 -0.35 24 24
VEGFC homodimer 0.016 0.046 -10000 0 -0.35 8 8
NCK1 0.021 0.023 -10000 0 -0.35 2 2
ROCK1 0.023 0.004 -10000 0 -10000 0 0
FAK1/Paxillin -0.028 0.15 -10000 0 -0.55 31 31
MAP3K13 -0.041 0.12 -10000 0 -0.49 28 28
PDPK1 -0.023 0.11 0.25 1 -0.45 28 29
IL6-mediated signaling events

Figure S70.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S70.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.072 0.15 0.45 8 -0.63 5 13
CRP 0.089 0.18 0.49 26 -0.65 4 30
cell cycle arrest 0.065 0.16 0.46 7 -0.61 9 16
TIMP1 0.063 0.15 0.44 5 -0.62 7 12
IL6ST -0.025 0.13 -10000 0 -0.34 74 74
Rac1/GDP 0.021 0.12 0.27 6 -0.34 30 36
AP1 0.014 0.14 0.37 1 -0.53 12 13
GAB2 0.02 0.033 -10000 0 -0.35 4 4
TNFSF11 0.077 0.16 0.45 7 -0.63 5 12
HSP90B1 0.043 0.094 -10000 0 -0.65 6 6
GAB1 0.02 0.033 -10000 0 -0.35 4 4
MAPK14 -0.005 0.12 0.24 1 -0.38 27 28
AKT1 0.025 0.061 0.25 1 -0.39 6 7
FOXO1 0.026 0.061 0.32 1 -0.38 5 6
MAP2K6 -0.007 0.11 0.22 6 -0.36 29 35
mol:GTP 0.001 0.001 -10000 0 -10000 0 0
MAP2K4 0.033 0.13 0.3 11 -0.34 23 34
MITF -0.015 0.13 0.22 7 -0.36 44 51
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0.021 0.007 -10000 0 -10000 0 0
A2M 0.001 0.15 -10000 0 -1.1 9 9
CEBPB 0.026 0.007 -10000 0 -10000 0 0
GRB2/SOS1/GAB family/SHP2 0.021 0.11 -10000 0 -0.52 11 11
STAT3 0.061 0.17 0.46 7 -0.63 10 17
STAT1 0.024 0.059 -10000 0 -0.82 2 2
CEBPD 0.073 0.16 0.46 8 -0.75 4 12
PIK3CA 0.02 0.018 -10000 0 -0.35 1 1
PI3K 0.028 0.03 -10000 0 -0.24 5 5
JUN 0.018 0.043 -10000 0 -0.35 7 7
PIAS3/MITF -0.014 0.13 0.27 1 -0.33 46 47
MAPK11 -0.005 0.11 0.24 1 -0.37 25 26
STAT3 (dimer)/FOXO1 0.065 0.15 0.41 10 -0.51 10 20
GRB2/SOS1/GAB family 0.025 0.12 -10000 0 -0.34 26 26
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.01 0.11 0.2 6 -0.26 60 66
GRB2 0.022 0.006 -10000 0 -10000 0 0
JAK2 0.016 0.049 -10000 0 -0.35 9 9
LBP 0.082 0.17 0.48 17 -0.63 6 23
PIK3R1 0.019 0.037 -10000 0 -0.35 5 5
JAK1 0.024 0.019 -10000 0 -0.34 1 1
MYC 0.078 0.2 0.46 14 -0.89 10 24
FGG 0.062 0.16 0.46 9 -0.6 6 15
macrophage differentiation 0.065 0.16 0.46 7 -0.61 9 16
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 0.011 0.12 0.24 1 -0.24 65 66
JUNB 0.061 0.17 0.43 5 -0.82 8 13
FOS -0.086 0.17 -10000 0 -0.35 152 152
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.001 0.12 0.26 4 -0.37 31 35
STAT1/PIAS1 0.033 0.12 0.3 6 -0.32 25 31
GRB2/SOS1/GAB family/SHP2/PI3K 0.028 0.061 -10000 0 -0.4 6 6
STAT3 (dimer) 0.063 0.17 0.46 7 -0.64 9 16
PRKCD 0.048 0.14 0.35 16 -0.44 10 26
IL6R -0.006 0.096 -10000 0 -0.35 38 38
SOCS3 -0.012 0.13 -10000 0 -0.63 8 8
gp130 (dimer)/JAK1/JAK1/LMO4 0.02 0.092 -10000 0 -0.2 75 75
Rac1/GTP 0.026 0.12 0.27 7 -0.33 29 36
HCK 0.025 0.03 0.28 7 -10000 0 7
MAPKKK cascade 0.036 0.11 0.31 1 -0.55 11 12
bone resorption 0.077 0.16 0.45 7 -0.6 5 12
IRF1 0.061 0.15 0.5 4 -0.68 4 8
mol:GDP 0.004 0.11 0.24 7 -0.35 29 36
SOS1 0.023 0.004 -10000 0 -10000 0 0
VAV1 0 0.11 0.24 7 -0.35 29 36
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.021 0.15 -10000 0 -0.45 43 43
PTPN11 0.022 0.065 -10000 0 -0.66 4 4
IL6/IL6RA 0.008 0.091 0.22 6 -0.26 48 54
gp130 (dimer)/TYK2/TYK2/LMO4 0.015 0.087 -10000 0 -0.2 69 69
gp130 (dimer)/JAK2/JAK2/LMO4 0.012 0.095 -10000 0 -0.2 80 80
IL6 0.022 0.072 0.29 9 -0.35 14 23
PIAS3 0.019 0.009 -10000 0 -10000 0 0
PTPRE 0 0.03 0.26 1 -0.35 1 2
PIAS1 0.022 0.005 -10000 0 -10000 0 0
RAC1 0.023 0.005 -10000 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.019 0.11 0.2 2 -0.27 66 68
LMO4 0.029 0.012 -10000 0 -10000 0 0
STAT3 (dimer)/PIAS3 0.036 0.15 0.42 1 -0.59 10 11
MCL1 0.06 0.1 0.37 8 -0.43 3 11
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

Figure S71.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S71.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HIF3A -0.12 0.18 0.28 2 -0.35 203 205
oxygen homeostasis 0 0 -10000 0 -10000 0 0
TCEB2 0.022 0.005 -10000 0 -10000 0 0
TCEB1 0.021 0.007 -10000 0 -10000 0 0
HIF1A/p53 0.024 0.062 0.25 1 -0.26 16 17
HIF1A 0.007 0.055 -10000 0 -0.27 16 16
COPS5 0.021 0.007 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 0.055 0.029 -10000 0 -0.18 1 1
FIH (dimer) 0.022 0.005 -10000 0 -10000 0 0
CDKN2A 0.12 0.13 0.28 207 -10000 0 207
ARNT/IPAS -0.058 0.12 0.21 2 -0.24 158 160
HIF1AN 0.022 0.005 -10000 0 -10000 0 0
GNB2L1 0.022 0.004 -10000 0 -10000 0 0
HIF1A/ARNT 0.01 0.051 -10000 0 -0.26 13 13
CUL2 0.022 0.004 -10000 0 -10000 0 0
OS9 0.023 0.001 -10000 0 -10000 0 0
RACK1/Elongin B/Elongin C 0.041 0.016 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF1A/Hsp90 0.023 0.061 -10000 0 -0.26 17 17
PHD1-3/OS9 0.047 0.03 0.21 3 -0.19 1 4
HIF1A/RACK1/Elongin B/Elongin C 0.039 0.059 -10000 0 -0.25 14 14
VHL 0.022 0.017 -10000 0 -0.35 1 1
HSP90AA1 0.022 0.004 -10000 0 -10000 0 0
HIF1A/JAB1 0.021 0.058 -10000 0 -0.26 13 13
EGLN3 0.023 0.026 0.28 3 -0.35 1 4
EGLN2 0.022 0.004 -10000 0 -10000 0 0
EGLN1 0.019 0.009 -10000 0 -10000 0 0
TP53 0.021 0.006 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.018 0.097 -10000 0 -0.53 15 15
ARNT 0.018 0.01 -10000 0 -10000 0 0
ARD1A 0 0 -10000 0 -10000 0 0
RBX1 0.022 0.006 -10000 0 -10000 0 0
HIF1A/p19ARF 0.082 0.1 0.25 37 -0.26 16 53
Canonical Wnt signaling pathway

Figure S72.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S72.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.026 0.024 0.22 4 -10000 0 4
AES 0.024 0.021 0.2 3 -10000 0 3
FBXW11 0.022 0.004 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -10000 0 0
LRP6/FZD1 0.031 0.022 -10000 0 -0.25 3 3
SMAD4 0.022 0.005 -10000 0 -10000 0 0
DKK2 0.001 0.088 0.28 2 -0.35 30 32
TLE1 0.024 0.021 0.2 4 -10000 0 4
MACF1 0.022 0.004 -10000 0 -10000 0 0
CTNNB1 0.008 0.083 0.31 7 -0.34 8 15
WIF1 0.06 0.15 0.28 124 -0.35 32 156
beta catenin/RanBP3 0.016 0.12 0.42 29 -0.49 1 30
KREMEN2 0.045 0.074 0.28 46 -10000 0 46
DKK1 0.069 0.11 0.28 104 -0.35 6 110
beta catenin/beta TrCP1 0.016 0.079 0.29 6 -0.31 8 14
FZD1 0.02 0.029 -10000 0 -0.35 3 3
AXIN2 -0.048 0.27 0.64 8 -1.2 26 34
AXIN1 0.022 0.005 -10000 0 -10000 0 0
RAN 0.023 0.003 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.006 0.11 -10000 0 -0.57 16 16
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 -0.026 0.18 0.3 2 -0.57 37 39
Axin1/APC/GSK3 0.005 0.056 0.24 3 -0.32 4 7
Axin1/APC/GSK3/beta catenin/Macf1 0.011 0.066 0.29 4 -0.36 7 11
HNF1A 0.029 0.037 0.25 12 -10000 0 12
CTBP1 0.024 0.021 0.2 3 -10000 0 3
MYC 0.066 0.28 0.59 77 -1.1 10 87
RANBP3 0.022 0.006 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.042 0.078 0.21 42 -0.2 30 72
NKD1 0.033 0.081 0.28 36 -0.35 8 44
TCF4 0.012 0.071 0.2 4 -0.35 18 22
TCF3 0.024 0.022 0.2 4 -10000 0 4
WNT1/LRP6/FZD1/Axin1 0.054 0.03 0.21 1 -0.19 3 4
Ran/GTP 0.017 0.003 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES -0.003 0.14 0.47 22 -0.43 13 35
LEF1 0.022 0.04 0.22 5 -0.33 4 9
DVL1 0.009 0.061 0.24 2 -0.53 4 6
CSNK2A1 0.022 0.004 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES -0.036 0.19 -10000 0 -0.55 47 47
DKK1/LRP6/Kremen 2 0.083 0.083 0.21 138 -0.2 6 144
LRP6 0.023 0.004 -10000 0 -10000 0 0
CSNK1A1 0.025 0.022 0.22 3 -10000 0 3
NLK 0.02 0.011 -10000 0 -10000 0 0
CCND1 0.003 0.11 0.57 10 -0.6 3 13
WNT1 0.024 0.031 0.28 7 -10000 0 7
GSK3A 0.023 0.004 -10000 0 -10000 0 0
GSK3B 0.022 0.004 -10000 0 -10000 0 0
FRAT1 0.022 0.006 -10000 0 -10000 0 0
PPP2R5D 0.015 0.047 0.25 7 -0.27 3 10
APC -0.01 0.043 0.18 21 -10000 0 21
WNT1/LRP6/FZD1 0.002 0.061 0.18 22 -0.2 6 28
CREBBP 0.024 0.021 0.19 4 -10000 0 4
IL2 signaling events mediated by STAT5

Figure S73.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S73.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GAB2 0.02 0.033 -10000 0 -0.35 4 4
ELF1 0.027 0.039 -10000 0 -0.33 4 4
CCNA2 0.076 0.1 0.28 108 -10000 0 108
PIK3CA 0.02 0.018 -10000 0 -0.35 1 1
JAK3 0.024 0.023 0.28 4 -10000 0 4
PIK3R1 0.019 0.037 -10000 0 -0.35 5 5
JAK1 0.022 0.017 -10000 0 -0.35 1 1
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.038 0.077 -10000 0 -0.41 5 5
SHC1 0.019 0.009 -10000 0 -10000 0 0
SP1 -0.036 0.13 -10000 0 -0.31 96 96
IL2RA 0.016 0.052 -10000 0 -0.61 1 1
IL2RB 0.021 0.017 -10000 0 -0.35 1 1
SOS1 0.023 0.004 -10000 0 -10000 0 0
IL2RG 0.024 0.04 0.28 6 -0.35 3 9
G1/S transition of mitotic cell cycle -0.091 0.27 0.29 4 -0.61 97 101
PTPN11 0.023 0.003 -10000 0 -10000 0 0
CCND2 -0.096 0.24 -10000 0 -0.61 90 90
LCK 0.024 0.028 0.28 4 -0.35 1 5
GRB2 0.022 0.006 -10000 0 -10000 0 0
IL2 0.027 0.045 0.28 16 -10000 0 16
CDK6 0.014 0.056 -10000 0 -0.35 12 12
CCND3 0.04 0.082 0.35 2 -0.46 2 4
BCR signaling pathway

Figure S74.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S74.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
JUN 0.008 0.12 0.32 10 -0.32 35 45
IKBKB 0.021 0.087 0.26 13 -0.28 12 25
AKT1 0.013 0.099 0.27 32 -0.21 17 49
IKBKG 0.018 0.081 0.22 10 -0.28 12 22
CALM1 0.011 0.097 0.21 13 -0.33 12 25
PIK3CA 0.02 0.018 -10000 0 -0.35 1 1
MAP3K1 0.001 0.16 0.34 9 -0.44 42 51
MAP3K7 0.023 0.003 -10000 0 -10000 0 0
mol:Ca2+ 0.013 0.1 0.22 10 -0.35 12 22
DOK1 0.023 0.003 -10000 0 -10000 0 0
AP-1 -0.006 0.09 0.25 9 -0.22 19 28
LYN 0.021 0.007 -10000 0 -10000 0 0
BLNK 0.021 0.026 0.28 1 -0.35 2 3
SHC1 0.019 0.009 -10000 0 -10000 0 0
BCR complex 0.034 0.085 0.21 49 -0.26 25 74
CD22 -0.025 0.12 0.23 4 -0.46 27 31
CAMK2G 0.016 0.098 0.26 16 -0.31 11 27
CSNK2A1 0.022 0.004 -10000 0 -10000 0 0
INPP5D 0.022 0.017 -10000 0 -0.35 1 1
SHC/GRB2/SOS1 0.017 0.041 -10000 0 -0.31 1 1
GO:0007205 0.013 0.1 0.22 10 -0.36 12 22
SYK 0.022 0.013 0.28 1 -10000 0 1
ELK1 0.011 0.1 0.24 8 -0.34 13 21
NFATC1 0.003 0.13 0.27 15 -0.37 29 44
B-cell antigen/BCR complex 0.034 0.085 0.21 49 -0.26 25 74
PAG1/CSK 0.029 0.021 -10000 0 -0.24 2 2
NFKBIB 0.021 0.046 0.14 15 -0.12 23 38
HRAS 0.015 0.094 0.23 12 -0.31 15 27
NFKBIA 0.022 0.045 0.14 15 -0.12 23 38
NF-kappa-B/RelA/I kappa B beta 0.025 0.04 0.14 15 -0.13 1 16
RasGAP/Csk 0.05 0.077 0.35 1 -0.19 25 26
mol:GDP 0.011 0.1 0.21 10 -0.34 13 23
PTEN 0.021 0.006 -10000 0 -10000 0 0
CD79B 0.005 0.078 -10000 0 -0.35 24 24
NF-kappa-B/RelA/I kappa B alpha 0.025 0.04 0.14 15 -0.13 1 16
GRB2 0.022 0.006 -10000 0 -10000 0 0
PI3K/BCAP/CD19 0.01 0.16 0.37 7 -0.42 43 50
PIK3R1 0.018 0.037 -10000 0 -0.35 5 5
mol:IP3 0.016 0.096 0.22 10 -0.39 9 19
CSK 0.022 0.005 -10000 0 -10000 0 0
FOS -0.032 0.12 0.26 8 -0.32 29 37
CHUK 0.012 0.098 0.23 10 -0.35 20 30
IBTK 0.023 0.003 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 0.028 0.093 0.26 2 -0.31 10 12
PTPN6 -0.028 0.11 0.22 4 -0.45 25 29
RELA 0.022 0.004 -10000 0 -10000 0 0
BCL2A1 0.02 0.028 0.12 4 -10000 0 4
VAV2 0.008 0.12 0.46 1 -0.43 24 25
ubiquitin-dependent protein catabolic process 0.023 0.046 0.14 15 -0.12 23 38
BTK 0.006 0.12 -10000 0 -0.94 8 8
CD19 -0.003 0.095 0.2 4 -0.39 23 27
MAP4K1 0.028 0.041 0.29 12 -10000 0 12
CD72 0.024 0.02 0.28 3 -10000 0 3
PAG1 0.02 0.024 -10000 0 -0.35 2 2
MAPK14 0.005 0.14 0.31 12 -0.39 39 51
SH3BP5 -0.031 0.13 -10000 0 -0.35 74 74
PIK3AP1 0.019 0.1 0.26 9 -0.31 16 25
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 0.015 0.09 0.24 1 -0.46 9 10
RAF1 0.013 0.091 0.24 12 -0.31 13 25
RasGAP/p62DOK/SHIP 0.047 0.074 0.32 1 -0.19 26 27
CD79A 0.045 0.084 0.28 51 -0.35 4 55
re-entry into mitotic cell cycle -0.006 0.09 0.25 9 -0.22 19 28
RASA1 0.019 0.037 -10000 0 -0.35 5 5
MAPK3 0.012 0.081 0.24 11 -0.27 9 20
MAPK1 0.01 0.079 0.23 9 -0.28 9 18
CD72/SHP1 0.002 0.14 0.3 8 -0.43 25 33
NFKB1 0.022 0.017 -10000 0 -0.35 1 1
MAPK8 0.003 0.15 0.37 10 -0.38 42 52
actin cytoskeleton organization 0.009 0.12 0.32 9 -0.37 28 37
NF-kappa-B/RelA 0.05 0.079 0.25 15 -0.19 15 30
Calcineurin 0.024 0.089 0.24 1 -0.32 8 9
PI3K -0.021 0.096 0.15 1 -0.36 24 25
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 0.023 0.1 0.25 8 -0.32 19 27
SOS1 0.023 0.003 -10000 0 -10000 0 0
Bam32/HPK1 -0.015 0.23 -10000 0 -0.62 53 53
DAPP1 -0.038 0.24 -10000 0 -0.7 52 52
cytokine secretion 0.004 0.12 0.26 16 -0.35 29 45
mol:DAG 0.016 0.096 0.22 10 -0.39 9 19
PLCG2 0.02 0.021 0.28 1 -0.35 1 2
MAP2K1 0.011 0.084 0.23 11 -0.28 13 24
B-cell antigen/BCR complex/FcgammaRIIB 0.039 0.075 0.21 45 -0.22 20 65
mol:PI-3-4-5-P3 -0.015 0.083 0.19 9 -0.26 21 30
ETS1 0.013 0.094 0.26 17 -0.32 8 25
B-cell antigen/BCR complex/LYN/SYK/BLNK 0.058 0.073 0.35 1 -0.2 18 19
B-cell antigen/BCR complex/LYN 0 0.098 0.22 2 -0.4 24 26
MALT1 0.022 0.005 -10000 0 -10000 0 0
TRAF6 0.022 0.005 -10000 0 -10000 0 0
RAC1 0.007 0.12 0.35 4 -0.4 24 28
B-cell antigen/BCR complex/LYN/SYK 0.007 0.13 0.34 3 -0.41 26 29
CARD11 0.013 0.1 0.25 12 -0.34 14 26
FCGR2B 0.018 0.027 0.28 1 -0.35 2 3
PPP3CA 0.022 0.005 -10000 0 -10000 0 0
BCL10 0.023 0.002 -10000 0 -10000 0 0
IKK complex 0.021 0.055 0.17 31 -0.12 12 43
PTPRC 0.015 0.045 0.28 1 -0.35 7 8
PDPK1 0.001 0.083 0.24 23 -0.21 14 37
PPP3CB 0.022 0.005 -10000 0 -10000 0 0
PPP3CC 0.017 0.033 -10000 0 -0.35 4 4
POU2F2 0.019 0.031 0.14 8 -10000 0 8
BARD1 signaling events

Figure S75.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S75.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BARD1/CSTF1 0.026 0.041 -10000 0 -0.24 11 11
ATM 0.022 0.005 -10000 0 -10000 0 0
UBE2D3 0.022 0.004 -10000 0 -10000 0 0
PRKDC 0.021 0.007 -10000 0 -10000 0 0
ATR 0.022 0.005 -10000 0 -10000 0 0
UBE2L3 0.022 0.005 -10000 0 -10000 0 0
FANCD2 0.015 0.012 0.24 1 -10000 0 1
protein ubiquitination 0.093 0.079 0.21 36 -0.17 10 46
XRCC5 0.023 0.003 -10000 0 -10000 0 0
XRCC6 0.022 0.006 -10000 0 -10000 0 0
M/R/N Complex 0.041 0.016 -10000 0 -10000 0 0
MRE11A 0.022 0.004 -10000 0 -10000 0 0
DNA-PK 0.04 0.017 -10000 0 -10000 0 0
FA complex/FANCD2/Ubiquitin 0.01 0.096 -10000 0 -0.36 23 23
FANCF 0.021 0.023 -10000 0 -0.35 2 2
BRCA1 0.022 0.005 -10000 0 -10000 0 0
CCNE1 0.13 0.13 0.29 211 -10000 0 211
CDK2/Cyclin E1 0.1 0.089 0.22 201 -10000 0 201
FANCG 0.022 0.005 -10000 0 -10000 0 0
BRCA1/BACH1/BARD1 0.026 0.041 -10000 0 -0.24 11 11
FANCE 0.023 0.004 -10000 0 -10000 0 0
FANCC 0.022 0.006 -10000 0 -10000 0 0
NBN 0.021 0.007 -10000 0 -10000 0 0
FANCA 0.078 0.11 0.28 116 -10000 0 116
DNA repair 0.011 0.077 0.26 6 -0.31 13 19
BRCA1/BARD1/ubiquitin 0.026 0.041 -10000 0 -0.24 11 11
BARD1/DNA-PK 0.045 0.041 -10000 0 -0.19 11 11
FANCL 0.023 0.003 -10000 0 -10000 0 0
mRNA polyadenylation -0.026 0.041 0.24 11 -10000 0 11
BRCA1/BARD1/CTIP/M/R/N Complex 0.011 0.049 -10000 0 -0.2 21 21
BRCA1/BACH1/BARD1/TopBP1 0.038 0.038 -10000 0 -0.21 11 11
BRCA1/BARD1/P53 0.046 0.04 -10000 0 -0.19 11 11
BARD1/CSTF1/BRCA1 0.037 0.039 -10000 0 -0.21 11 11
BRCA1/BACH1 0.022 0.005 -10000 0 -10000 0 0
BARD1 0.015 0.054 -10000 0 -0.35 11 11
PCNA 0.022 0.004 -10000 0 -10000 0 0
BRCA1/BARD1/UbcH5C 0.038 0.038 -10000 0 -0.21 11 11
BRCA1/BARD1/UbcH7 0.037 0.039 -10000 0 -0.21 11 11
BRCA1/BARD1/RAD51/PCNA 0.084 0.081 0.21 128 -0.18 11 139
BARD1/DNA-PK/P53 0.051 0.044 -10000 0 -0.18 11 11
BRCA1/BARD1/Ubiquitin 0.026 0.041 -10000 0 -0.24 11 11
BRCA1/BARD1/CTIP 0.028 0.034 -10000 0 -0.19 11 11
FA complex 0.025 0.059 0.2 5 -0.22 7 12
BARD1/EWS 0.026 0.041 -10000 0 -0.24 11 11
RBBP8 -0.011 0.003 -10000 0 -10000 0 0
TP53 0.021 0.006 -10000 0 -10000 0 0
TOPBP1 0.023 0.004 -10000 0 -10000 0 0
G1/S transition of mitotic cell cycle -0.045 0.04 0.19 11 -10000 0 11
BRCA1/BARD1 0.1 0.085 0.23 36 -0.18 10 46
CSTF1 0.022 0.005 -10000 0 -10000 0 0
BARD1/EWS-Fli1 0.011 0.037 -10000 0 -0.24 11 11
CDK2 0.023 0.004 -10000 0 -10000 0 0
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 0.097 0.12 0.28 151 -10000 0 151
RAD50 0.023 0.003 -10000 0 -10000 0 0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme 0.026 0.041 -10000 0 -0.24 11 11
EWSR1 0.022 0.006 -10000 0 -10000 0 0
Hedgehog signaling events mediated by Gli proteins

Figure S76.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S76.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.023 0.004 -10000 0 -10000 0 0
HDAC2 0.023 0.003 -10000 0 -10000 0 0
GNB1/GNG2 0.037 0.039 0.2 1 -0.21 11 12
forebrain development -0.091 0.21 -10000 0 -0.48 92 92
GNAO1 -0.066 0.16 -10000 0 -0.35 120 120
SMO/beta Arrestin2 0.026 0.03 -10000 0 -0.24 4 4
SMO 0.017 0.034 -10000 0 -0.35 4 4
ARRB2 0.019 0.011 -10000 0 -10000 0 0
GLI3/SPOP -0.038 0.13 -10000 0 -0.42 16 16
mol:GTP 0 0.001 -10000 0 -10000 0 0
GSK3B 0.022 0.004 -10000 0 -10000 0 0
GNAI2 0.022 0.007 -10000 0 -10000 0 0
SIN3/HDAC complex 0.052 0.02 -10000 0 -10000 0 0
GNAI1 0.016 0.046 -10000 0 -0.35 8 8
XPO1 0.021 0.012 -10000 0 -10000 0 0
GLI1/Su(fu) -0.062 0.17 -10000 0 -0.54 40 40
SAP30 0.022 0.004 -10000 0 -10000 0 0
mol:GDP 0.017 0.034 -10000 0 -0.35 4 4
MIM/GLI2A 0.015 0.032 -10000 0 -10000 0 0
IFT88 0.022 0.005 -10000 0 -10000 0 0
GNAI3 0.023 0.005 -10000 0 -10000 0 0
GLI2 -0.038 0.1 0.18 2 -0.34 22 24
GLI3 -0.046 0.13 -10000 0 -0.45 16 16
CSNK1D 0.022 0.006 -10000 0 -10000 0 0
CSNK1E 0.021 0.006 -10000 0 -10000 0 0
SAP18 0.022 0.005 -10000 0 -10000 0 0
embryonic digit morphogenesis 0.022 0.005 -10000 0 -10000 0 0
GNG2 0.017 0.05 0.28 1 -0.35 9 10
Gi family/GTP -0.042 0.11 -10000 0 -0.21 129 129
SIN3B 0.022 0.005 -10000 0 -10000 0 0
SIN3A 0.022 0.005 -10000 0 -10000 0 0
GLI3/Su(fu) -0.027 0.11 -10000 0 -0.4 18 18
GLI2/Su(fu) -0.028 0.1 -10000 0 -0.32 32 32
FOXA2 -0.07 0.28 -10000 0 -0.91 50 50
neural tube patterning -0.091 0.21 -10000 0 -0.48 92 92
SPOP 0.022 0.005 -10000 0 -10000 0 0
Su(fu)/PIAS1 0.021 0.035 -10000 0 -10000 0 0
GNB1 0.022 0.004 -10000 0 -10000 0 0
CSNK1G2 0.021 0.006 -10000 0 -10000 0 0
CSNK1G3 0.022 0.004 -10000 0 -10000 0 0
MTSS1 0.015 0.032 -10000 0 -10000 0 0
embryonic limb morphogenesis -0.091 0.21 -10000 0 -0.48 92 92
SUFU 0.013 0.016 -10000 0 -0.14 4 4
LGALS3 0.021 0.023 -10000 0 -0.35 2 2
catabolic process -0.061 0.15 -10000 0 -0.34 72 72
GLI3A/CBP -0.029 0.12 -10000 0 -0.31 84 84
KIF3A 0.022 0.017 -10000 0 -0.35 1 1
GLI1 -0.093 0.21 -10000 0 -0.49 92 92
RAB23 0.019 0.037 -10000 0 -0.35 5 5
CSNK1A1 0.022 0.004 -10000 0 -10000 0 0
IFT172 0.022 0.004 -10000 0 -10000 0 0
RBBP7 0.023 0.004 -10000 0 -10000 0 0
Su(fu)/Galectin3 0.019 0.041 -10000 0 -0.17 2 2
GNAZ 0.011 0.062 -10000 0 -0.35 15 15
RBBP4 0.02 0.028 -10000 0 -0.35 3 3
CSNK1G1 0.022 0.005 -10000 0 -10000 0 0
PIAS1 0.022 0.005 -10000 0 -10000 0 0
PRKACA 0.022 0.005 -10000 0 -10000 0 0
GLI2/SPOP -0.028 0.11 -10000 0 -0.34 24 24
STK36 0.021 0.012 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP -0.043 0.1 -10000 0 -0.31 33 33
PTCH1 -0.083 0.19 -10000 0 -0.58 37 37
MIM/GLI1 -0.085 0.22 -10000 0 -0.54 76 76
CREBBP -0.029 0.12 -10000 0 -0.31 84 84
Su(fu)/SIN3/HDAC complex 0.006 0.084 0.19 1 -0.37 17 18
mTOR signaling pathway

Figure S77.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S77.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GBL 0 0 -10000 0 -10000 0 0
MKNK1 0.023 0.004 -10000 0 -10000 0 0
mol:PIP3 -0.029 0.069 -10000 0 -0.25 45 45
FRAP1 0.009 0.055 0.28 2 -0.39 4 6
AKT1 -0.01 0.078 0.16 38 -0.22 41 79
INSR 0.021 0.006 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.025 0.008 -10000 0 -10000 0 0
mol:GTP 0.011 0.073 0.2 7 -0.19 37 44
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit -0.001 0.036 -10000 0 -0.17 9 9
TSC2 0.022 0.005 -10000 0 -10000 0 0
RHEB/GDP -0.001 0.051 -10000 0 -0.17 34 34
TSC1 0.021 0.017 -10000 0 -0.35 1 1
Insulin Receptor/IRS1 -0.012 0.093 -10000 0 -0.28 57 57
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA 0.006 0.045 -10000 0 -0.2 9 9
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0.022 0.005 -10000 0 -10000 0 0
RPS6KB1 0.007 0.08 0.26 9 -0.3 11 20
MAP3K5 0.005 0.034 0.2 8 -0.21 6 14
PIK3R1 0.019 0.037 -10000 0 -0.35 5 5
apoptosis 0.005 0.034 0.2 8 -0.21 6 14
mol:LY294002 0 0 0.001 1 -0.001 57 58
EIF4B 0.008 0.077 0.25 11 -0.27 11 22
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.022 0.069 0.26 6 -0.26 8 14
eIF4E/eIF4G1/eIF4A1 0.007 0.03 -10000 0 -0.26 3 3
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K 0.001 0.087 -10000 0 -0.26 49 49
mTOR/RHEB/GTP/Raptor/GBL 0.001 0.053 0.2 14 -0.14 8 22
FKBP1A 0.023 0.004 -10000 0 -10000 0 0
RHEB/GTP 0.014 0.062 -10000 0 -0.17 33 33
mol:Amino Acids 0 0 0.001 1 -0.001 57 58
FKBP12/Rapamycin 0.017 0.004 -10000 0 -10000 0 0
PDPK1 -0.02 0.078 0.15 33 -0.23 45 78
EIF4E 0.022 0.005 -10000 0 -10000 0 0
ASK1/PP5C 0.024 0.084 -10000 0 -0.54 8 8
mTOR/RHEB/GTP/Raptor/GBL/eIF4E -0.004 0.08 -10000 0 -0.3 24 24
TSC1/TSC2 0.013 0.08 0.23 8 -0.2 37 45
tumor necrosis factor receptor activity 0 0 0.001 57 -0.001 1 58
RPS6 0.022 0.005 -10000 0 -10000 0 0
PPP5C 0.023 0.004 -10000 0 -10000 0 0
EIF4G1 0.021 0.007 -10000 0 -10000 0 0
IRS1 -0.026 0.094 -10000 0 -0.29 57 57
INS 0.016 0.004 -10000 0 -10000 0 0
PTEN 0.021 0.006 -10000 0 -10000 0 0
PDK2 -0.019 0.078 0.15 35 -0.23 44 79
EIF4EBP1 -0.021 0.22 -10000 0 -1 24 24
PIK3CA 0.02 0.018 -10000 0 -0.35 1 1
PPP2R5D 0.01 0.061 0.27 9 -0.36 4 13
peptide biosynthetic process -0.012 0.017 0.18 4 -10000 0 4
RHEB 0.022 0.005 -10000 0 -10000 0 0
EIF4A1 0.021 0.006 -10000 0 -10000 0 0
mol:Rapamycin 0 0.001 0.003 56 -0.002 1 57
EEF2 -0.012 0.017 0.18 4 -10000 0 4
eIF4E/4E-BP1 -0.01 0.21 -10000 0 -0.94 24 24
EPO signaling pathway

Figure S78.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S78.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0 0.11 -10000 0 -0.42 6 6
CRKL -0.01 0.065 0.21 8 -0.24 5 13
mol:DAG 0.003 0.066 0.18 3 -0.25 17 20
HRAS 0.013 0.092 0.27 20 -0.23 5 25
MAPK8 0 0.072 0.18 57 -0.19 18 75
RAP1A -0.01 0.066 0.19 14 -0.23 6 20
GAB1 -0.012 0.067 0.18 13 -0.25 7 20
MAPK14 0.001 0.069 0.18 57 -0.18 13 70
EPO 0.009 0.066 0.29 1 -0.35 15 16
PLCG1 0.003 0.067 0.19 1 -0.25 17 18
EPOR/TRPC2/IP3 Receptors 0.021 0.037 0.29 7 -10000 0 7
RAPGEF1 0.022 0.006 -10000 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 0.031 0.055 0.21 8 -0.2 17 25
GAB1/SHC/GRB2/SOS1 0.018 0.059 0.26 1 -0.23 5 6
EPO/EPOR (dimer) 0.021 0.057 0.22 7 -0.25 15 22
IRS2 -0.031 0.083 0.22 7 -0.26 15 22
STAT1 -0.001 0.086 -10000 0 -0.25 44 44
STAT5B 0 0.079 0.19 1 -0.26 21 22
cell proliferation 0.002 0.08 0.2 61 -0.18 16 77
GAB1/SHIP/PIK3R1/SHP2/SHC 0.012 0.059 -10000 0 -0.24 8 8
TEC -0.011 0.065 0.19 14 -0.24 5 19
SOCS3 0.021 0.024 -10000 0 -0.35 2 2
STAT1 (dimer) -0.001 0.086 0.28 1 -0.24 45 46
JAK2 0.013 0.05 -10000 0 -0.34 9 9
PIK3R1 0.018 0.037 -10000 0 -0.35 5 5
EPO/EPOR (dimer)/JAK2 0.039 0.071 -10000 0 -0.19 22 22
EPO/EPOR 0.021 0.057 0.22 7 -0.25 15 22
LYN 0.017 0.015 -10000 0 -10000 0 0
TEC/VAV2 0.015 0.064 0.27 3 -0.24 5 8
elevation of cytosolic calcium ion concentration 0.021 0.037 0.29 7 -10000 0 7
SHC1 0.019 0.009 -10000 0 -10000 0 0
EPO/EPOR (dimer)/LYN 0.03 0.054 0.21 6 -0.2 14 20
mol:IP3 0.003 0.066 0.18 3 -0.25 17 20
PI3K regualtory subunit polypeptide 1/IRS2/SHIP -0.001 0.095 0.28 4 -0.26 17 21
SH2B3 0.019 0.024 -10000 0 -0.35 1 1
NFKB1 0.001 0.07 0.18 57 -0.18 15 72
EPO/EPOR (dimer)/JAK2/SOCS3 0.001 0.053 0.2 1 -0.2 27 28
PTPN6 -0.008 0.065 0.16 40 -0.19 20 60
TEC/VAV2/GRB2 0.023 0.063 0.27 2 -0.23 5 7
EPOR 0.021 0.037 0.29 7 -10000 0 7
INPP5D 0.022 0.017 -10000 0 -0.35 1 1
mol:GDP 0.018 0.059 0.26 1 -0.24 5 6
SOS1 0.023 0.003 -10000 0 -10000 0 0
PLCG2 0.02 0.021 0.28 1 -0.35 1 2
CRKL/CBL/C3G 0.024 0.065 0.27 3 -0.23 5 8
VAV2 -0.011 0.064 0.19 13 -0.24 5 18
CBL -0.01 0.065 0.19 13 -0.24 5 18
SHC/Grb2/SOS1 0.013 0.051 -10000 0 -0.24 4 4
STAT5A 0 0.078 0.19 1 -0.26 20 21
GRB2 0.022 0.006 -10000 0 -10000 0 0
STAT5 (dimer) 0.004 0.1 -10000 0 -0.31 38 38
LYN/PLCgamma2 0.024 0.023 0.21 1 -0.24 1 2
PTPN11 0.023 0.003 -10000 0 -10000 0 0
BTK -0.011 0.067 0.18 13 -0.27 5 18
BCL2 -0.042 0.24 -10000 0 -0.73 50 50
Class I PI3K signaling events mediated by Akt

Figure S79.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S79.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.01 0.014 0.3 1 -10000 0 1
BAD/BCL-XL/YWHAZ 0.03 0.017 0.21 1 -10000 0 1
CDKN1B 0.002 0.048 -10000 0 -0.29 7 7
CDKN1A 0.009 0.046 -10000 0 -0.29 8 8
FRAP1 0 0 -10000 0 -10000 0 0
PRKDC 0.021 0.007 -10000 0 -10000 0 0
FOXO3 0.008 0.037 -10000 0 -0.28 6 6
AKT1 0.007 0.036 -10000 0 -0.3 7 7
BAD 0.022 0.004 -10000 0 -10000 0 0
AKT3 -0.069 0.12 -10000 0 -0.26 151 151
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 0.006 0.042 -10000 0 -0.29 8 8
AKT1/ASK1 0.028 0.051 0.23 2 -0.28 8 10
BAD/YWHAZ 0.039 0.018 -10000 0 -10000 0 0
RICTOR 0.021 0.023 -10000 0 -0.35 2 2
RAF1 0.022 0.004 -10000 0 -10000 0 0
JNK cascade -0.026 0.047 0.27 8 -10000 0 8
TSC1 0.009 0.024 -10000 0 -0.27 2 2
YWHAZ 0.021 0.007 -10000 0 -10000 0 0
AKT1/RAF1 0.032 0.051 0.24 1 -0.28 7 8
EP300 0.021 0.006 -10000 0 -10000 0 0
mol:GDP 0.009 0.04 -10000 0 -0.29 8 8
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 0.007 0.039 -10000 0 -0.29 7 7
YWHAQ 0.022 0.005 -10000 0 -10000 0 0
TBC1D4 0.001 0.012 -10000 0 -0.19 2 2
MAP3K5 0.022 0.017 -10000 0 -0.35 1 1
MAPKAP1 0.022 0.005 -10000 0 -10000 0 0
negative regulation of cell cycle -0.045 0.078 0.39 7 -0.23 13 20
YWHAH 0.022 0.006 -10000 0 -10000 0 0
AKT1S1 0.007 0.042 -10000 0 -0.29 8 8
CASP9 0.009 0.036 -10000 0 -0.28 5 5
YWHAB 0.022 0.005 -10000 0 -10000 0 0
p27Kip1/KPNA1 0.022 0.067 0.29 6 -0.28 8 14
GBL 0 0 -10000 0 -10000 0 0
PDK1/Src/Hsp90 0.042 0.015 -10000 0 -10000 0 0
YWHAE 0.021 0.007 -10000 0 -10000 0 0
SRC 0.022 0.005 -10000 0 -10000 0 0
AKT2/p21CIP1 0.014 0.048 0.24 4 -0.26 7 11
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.005 0.048 -10000 0 -0.28 13 13
CHUK 0.009 0.04 -10000 0 -0.28 6 6
BAD/BCL-XL 0.03 0.043 0.26 1 -0.28 5 6
mTORC2 0.026 0.016 -10000 0 -0.18 2 2
AKT2 0.01 0.003 -10000 0 -10000 0 0
FOXO1-3a-4/14-3-3 family 0.053 0.09 0.26 15 -0.37 10 25
PDPK1 0.022 0.005 -10000 0 -10000 0 0
MDM2 0.008 0.041 0.19 3 -0.29 7 10
MAPKKK cascade -0.031 0.05 0.28 7 -0.24 1 8
MDM2/Cbp/p300 0.038 0.054 0.27 3 -0.26 8 11
TSC1/TSC2 0.007 0.039 0.26 4 -0.26 5 9
proteasomal ubiquitin-dependent protein catabolic process 0.036 0.052 0.26 3 -0.25 8 11
glucose import -0.08 0.091 0.2 5 -0.18 233 238
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.008 0.038 0.18 3 -0.18 11 14
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 -0.082 0.089 0.2 2 -0.18 233 235
GSK3A 0.008 0.043 -10000 0 -0.29 8 8
FOXO1 0.007 0.036 -10000 0 -0.29 6 6
GSK3B 0.008 0.043 -10000 0 -0.29 8 8
SFN 0.21 0.12 0.28 372 -10000 0 372
G1/S transition of mitotic cell cycle 0.014 0.057 0.24 10 -0.28 8 18
p27Kip1/14-3-3 family 0.054 0.084 0.27 5 -0.51 6 11
PRKACA 0.022 0.005 -10000 0 -10000 0 0
KPNA1 0.022 0.004 -10000 0 -10000 0 0
HSP90AA1 0.022 0.004 -10000 0 -10000 0 0
YWHAG 0.022 0.004 -10000 0 -10000 0 0
RHEB 0.022 0.005 -10000 0 -10000 0 0
CREBBP 0.022 0.005 -10000 0 -10000 0 0
Regulation of p38-alpha and p38-beta

Figure S80.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S80.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
RIP1/MEKK3 0.029 0.009 -10000 0 -10000 0 0
response to insulin stimulus 0 0 -10000 0 -10000 0 0
RIPK1 0.022 0.004 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.053 0.085 0.28 63 -10000 0 63
mol:GTP 0 0 -10000 0 -10000 0 0
MAP2K4 0.02 0.018 -10000 0 -0.35 1 1
RAC1-CDC42/GTP/PAK family -0.013 0.061 -10000 0 -0.17 65 65
response to UV 0 0 -10000 0 -10000 0 0
YES1 0.022 0.005 -10000 0 -10000 0 0
interleukin-1 receptor activity 0 0 -10000 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
MAP3K3 0.022 0.005 -10000 0 -10000 0 0
FYN 0.022 0.004 -10000 0 -10000 0 0
MAP3K12 0.02 0.033 -10000 0 -0.35 4 4
FGR 0.015 0.051 -10000 0 -0.35 10 10
p38 alpha/TAB1 -0.022 0.074 -10000 0 -0.29 26 26
PRKG1 -0.13 0.18 -10000 0 -0.35 215 215
DUSP8 0.018 0.037 -10000 0 -0.35 5 5
PGK/cGMP/p38 alpha -0.045 0.11 -10000 0 -0.29 41 41
apoptosis -0.022 0.07 -10000 0 -0.27 26 26
RAL/GTP 0.03 0.006 -10000 0 -10000 0 0
LYN 0.021 0.007 -10000 0 -10000 0 0
DUSP1 -0.064 0.16 -10000 0 -0.35 121 121
PAK1 0.022 0.004 -10000 0 -10000 0 0
SRC 0.022 0.005 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.051 0.021 -10000 0 -10000 0 0
TRAF6 0.022 0.005 -10000 0 -10000 0 0
RAC1 0.022 0.005 -10000 0 -10000 0 0
epidermal growth factor receptor activity 0 0 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
mol:cGMP 0 0 -10000 0 -10000 0 0
CCM2 0.023 0.004 -10000 0 -10000 0 0
RAC1-CDC42/GTP 0.029 0.008 -10000 0 -10000 0 0
MAPK11 0.02 0.098 0.26 10 -0.37 14 24
BLK 0.037 0.067 0.28 36 -10000 0 36
HCK 0.025 0.03 0.28 7 -10000 0 7
MAP2K3 0.021 0.006 -10000 0 -10000 0 0
DUSP16 0.023 0.003 -10000 0 -10000 0 0
DUSP10 0.019 0.008 -10000 0 -10000 0 0
TRAF6/MEKK3 0.027 0.008 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0.018 0.1 0.22 11 -0.36 18 29
positive regulation of innate immune response 0.023 0.11 0.27 13 -0.45 14 27
LCK 0.024 0.028 0.28 4 -0.35 1 5
p38alpha-beta/MKP7 0.03 0.11 0.27 10 -0.43 14 24
p38alpha-beta/MKP5 0.022 0.11 0.29 8 -0.43 14 22
PGK/cGMP -0.091 0.13 -10000 0 -0.24 215 215
PAK2 0.021 0.007 -10000 0 -10000 0 0
p38alpha-beta/MKP1 0.007 0.12 0.28 7 -0.37 27 34
CDC42 0.022 0.004 -10000 0 -10000 0 0
RALB 0.023 0.002 -10000 0 -10000 0 0
RALA 0.022 0.004 -10000 0 -10000 0 0
PAK3 -0.032 0.13 -10000 0 -0.35 74 74
IFN-gamma pathway

Figure S81.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S81.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.064 0.058 -10000 0 -0.17 10 10
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
CRKL 0.022 0.005 -10000 0 -10000 0 0
STAT1 (dimer)/Cbp/p300 0.037 0.038 0.27 2 -10000 0 2
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.041 0.038 -10000 0 -0.21 10 10
antigen processing and presentation of peptide antigen via MHC class I -0.032 0.055 -10000 0 -0.19 8 8
CaM/Ca2+ 0.062 0.053 -10000 0 -0.16 7 7
RAP1A 0.023 0.001 -10000 0 -10000 0 0
STAT1 (dimer)/SHP2 0.025 0.036 0.17 3 -0.16 9 12
AKT1 0.008 0.072 0.27 14 -0.28 1 15
MAP2K1 -0.01 0.04 0.2 8 -0.16 2 10
MAP3K11 -0.005 0.044 0.21 7 -0.17 6 13
IFNGR1 0.023 0.009 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKII -0.15 0.18 0.26 1 -0.32 254 255
Rap1/GTP -0.019 0.024 -10000 0 -10000 0 0
CRKL/C3G 0.031 0.01 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP 0.073 0.061 -10000 0 -0.18 10 10
CEBPB -0.008 0.13 0.3 5 -0.54 21 26
STAT3 0.022 0.006 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 0.049 0.15 -10000 0 -0.68 19 19
STAT1 -0.006 0.044 0.2 9 -10000 0 9
CALM1 0.022 0.004 -10000 0 -10000 0 0
IFN-gamma (dimer) 0.044 0.087 0.29 57 -10000 0 57
PIK3CA 0.02 0.018 -10000 0 -0.35 1 1
STAT1 (dimer)/PIAS1 0.017 0.044 0.27 3 -10000 0 3
CEBPB/PTGES2/Cbp/p300 0.011 0.081 -10000 0 -0.37 15 15
mol:Ca2+ 0.061 0.056 -10000 0 -0.17 10 10
MAPK3 -0.017 0.14 -10000 0 -0.64 22 22
STAT1 (dimer) -0.038 0.075 -10000 0 -0.27 7 7
MAPK1 -0.03 0.17 -10000 0 -0.68 31 31
JAK2 0.017 0.05 -10000 0 -0.35 9 9
PIK3R1 0.018 0.037 -10000 0 -0.35 5 5
JAK1 0.023 0.019 -10000 0 -0.35 1 1
CAMK2D 0.022 0.017 -10000 0 -0.35 1 1
DAPK1 0 0.087 0.28 3 -0.37 16 19
SMAD7 -0.011 0.05 0.18 12 -0.2 3 15
CBL/CRKL/C3G 0.032 0.041 0.27 3 -10000 0 3
PI3K 0.051 0.053 -10000 0 -0.18 9 9
IFNG 0.044 0.087 0.29 57 -10000 0 57
apoptosis -0.001 0.074 0.23 1 -0.3 17 18
CAMK2G 0.022 0.005 -10000 0 -10000 0 0
STAT3 (dimer) 0.022 0.006 -10000 0 -10000 0 0
CAMK2A -0.18 0.18 -10000 0 -0.35 280 280
CAMK2B 0.064 0.098 0.28 85 -0.35 1 86
FRAP1 0.006 0.068 0.23 20 -0.26 1 21
PRKCD 0.007 0.074 0.25 18 -0.29 1 19
RAP1B 0.023 0.002 -10000 0 -10000 0 0
negative regulation of cell growth -0.032 0.055 -10000 0 -0.19 8 8
PTPN2 0.022 0.004 -10000 0 -10000 0 0
EP300 0.022 0.006 -10000 0 -10000 0 0
IRF1 -0.004 0.046 0.28 5 -0.31 1 6
STAT1 (dimer)/PIASy 0.015 0.043 0.27 3 -10000 0 3
SOCS1 -0.015 0.2 -10000 0 -1 19 19
mol:GDP 0.029 0.038 0.25 3 -10000 0 3
CASP1 -0.01 0.05 0.18 12 -0.16 4 16
PTGES2 0.022 0.005 -10000 0 -10000 0 0
IRF9 0.009 0.04 0.18 4 -0.15 11 15
mol:PI-3-4-5-P3 0.037 0.044 -10000 0 -0.17 11 11
RAP1/GDP 0.029 0.031 -10000 0 -10000 0 0
CBL -0.006 0.043 0.2 8 -0.17 7 15
MAP3K1 -0.006 0.042 0.2 8 -0.17 7 15
PIAS1 0.022 0.005 -10000 0 -10000 0 0
PIAS4 0.021 0.006 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II -0.032 0.055 -10000 0 -0.19 8 8
PTPN11 -0.004 0.045 0.17 19 -0.17 10 29
CREBBP 0.022 0.005 -10000 0 -10000 0 0
RAPGEF1 0.022 0.006 -10000 0 -10000 0 0
Nectin adhesion pathway

Figure S82.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S82.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.009 0.07 -10000 0 -0.35 19 19
alphaV beta3 Integrin -0.013 0.1 0.21 2 -0.24 85 87
PTK2 -0.018 0.097 -10000 0 -0.37 23 23
positive regulation of JNK cascade 0.001 0.082 -10000 0 -0.27 30 30
CDC42/GDP 0.009 0.12 -10000 0 -0.37 35 35
Rac1/GDP 0.006 0.12 0.3 2 -0.37 35 37
RAP1B 0.023 0.002 -10000 0 -10000 0 0
RAP1A 0.023 0.001 -10000 0 -10000 0 0
CTNNB1 0.022 0.004 -10000 0 -10000 0 0
CDC42/GTP 0.006 0.1 -10000 0 -0.34 29 29
nectin-3/I-afadin 0.02 0.056 -10000 0 -0.24 22 22
RAPGEF1 -0.003 0.11 0.31 4 -0.4 27 31
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.008 0.11 -10000 0 -0.45 27 27
PDGFB-D/PDGFRB 0.009 0.07 -10000 0 -0.35 19 19
TLN1 -0.021 0.059 -10000 0 -0.27 23 23
Rap1/GTP -0.003 0.079 -10000 0 -0.3 27 27
IQGAP1 0.022 0.004 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.042 0.01 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin 0.02 0.056 -10000 0 -0.24 22 22
PVR 0.022 0.005 -10000 0 -10000 0 0
Necl-5(dimer) 0.022 0.005 -10000 0 -10000 0 0
mol:GDP -0.005 0.14 0.31 2 -0.45 35 37
MLLT4 0.022 0.005 -10000 0 -10000 0 0
PIK3CA 0.02 0.018 -10000 0 -0.35 1 1
PI3K 0.041 0.067 -10000 0 -0.2 31 31
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.032 0.015 0.21 2 -10000 0 2
positive regulation of lamellipodium assembly -0.005 0.097 -10000 0 -0.3 39 39
PVRL1 0.023 0.017 0.28 2 -10000 0 2
PVRL3 0.007 0.075 -10000 0 -0.35 22 22
PVRL2 0.022 0.005 -10000 0 -10000 0 0
PIK3R1 0.018 0.037 -10000 0 -0.35 5 5
CDH1 0.019 0.024 -10000 0 -0.35 2 2
CLDN1 -0.019 0.12 -10000 0 -0.35 56 56
JAM-A/CLDN1 0.013 0.082 -10000 0 -0.2 59 59
SRC -0.011 0.12 -10000 0 -0.48 30 30
ITGB3 -0.038 0.14 0.28 2 -0.35 85 87
nectin-1(dimer)/I-afadin/I-afadin 0.032 0.015 0.21 2 -10000 0 2
FARP2 0.001 0.14 0.32 1 -0.45 31 32
RAC1 0.022 0.005 -10000 0 -10000 0 0
CTNNA1 0.023 0.004 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) 0.032 0.051 -10000 0 -0.21 21 21
nectin-1/I-afadin 0.032 0.015 0.21 2 -10000 0 2
nectin-2/I-afadin 0.031 0.01 -10000 0 -10000 0 0
RAC1/GTP/IQGAP1/filamentous actin 0.029 0.008 -10000 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin 0.032 0.052 -10000 0 -0.21 22 22
CDC42/GTP/IQGAP1/filamentous actin 0.029 0.008 -10000 0 -10000 0 0
F11R 0.018 0.018 -10000 0 -0.35 1 1
positive regulation of filopodium formation 0.001 0.082 -10000 0 -0.27 30 30
alphaV/beta3 Integrin/Talin -0.021 0.11 0.3 3 -0.3 34 37
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.031 0.01 -10000 0 -10000 0 0
nectin-2(dimer)/I-afadin/I-afadin 0.031 0.01 -10000 0 -10000 0 0
PIP5K1C -0.016 0.065 -10000 0 -0.28 24 24
VAV2 -0.014 0.16 0.34 1 -0.49 40 41
RAP1/GDP 0.012 0.11 0.3 1 -0.35 31 32
ITGAV 0.023 0.003 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin 0.032 0.051 -10000 0 -0.21 21 21
nectin-3(dimer)/I-afadin/I-afadin 0.02 0.056 -10000 0 -0.24 22 22
Rac1/GTP -0.003 0.12 -10000 0 -0.36 39 39
PTPRM -0.013 0.075 -10000 0 -0.24 47 47
E-cadherin/beta catenin/alpha catenin 0.054 0.033 -10000 0 -0.18 2 2
adherens junction assembly 0 0 -10000 0 -10000 0 0
CDC42 0.022 0.004 -10000 0 -10000 0 0
IL1-mediated signaling events

Figure S83.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S83.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
UBC13/UEV1A 0.013 0.065 -10000 0 -0.24 31 31
PRKCZ 0.022 0.02 0.28 1 -0.35 1 2
MAP3K7IP2 0 0 -10000 0 -10000 0 0
ERC1 0.022 0.004 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 0.011 0.042 -10000 0 -0.22 12 12
IRAK/TOLLIP 0.009 0.049 -10000 0 -0.19 30 30
IKBKB 0.021 0.007 -10000 0 -10000 0 0
IKBKG 0.023 0.003 -10000 0 -10000 0 0
IL1 alpha/IL1R2 0.053 0.07 0.23 59 -0.25 4 63
IL1A 0.038 0.063 0.28 33 -10000 0 33
IL1B -0.014 0.028 -10000 0 -0.28 5 5
IRAK/TRAF6/p62/Atypical PKCs 0.036 0.058 -10000 0 -0.18 24 24
IL1R2 0.036 0.07 0.28 32 -0.35 4 36
IL1R1 0.016 0.049 -10000 0 -0.35 9 9
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.006 0.064 0.21 3 -0.26 16 19
TOLLIP 0.022 0.005 -10000 0 -10000 0 0
TICAM2 0.016 0.046 -10000 0 -0.35 8 8
MAP3K3 0.022 0.005 -10000 0 -10000 0 0
TAK1/TAB1/TAB2 0.015 0.002 -10000 0 -10000 0 0
IKK complex/ELKS 0.012 0.066 0.3 5 -0.33 3 8
JUN -0.014 0.065 0.17 36 -0.2 9 45
MAP3K7 0.023 0.003 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K 0.042 0.053 -10000 0 -0.21 15 15
IL1 alpha/IL1R1/IL1RAP/MYD88 0.055 0.055 -10000 0 -0.21 9 9
PIK3R1 0.018 0.037 -10000 0 -0.35 5 5
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 0.063 0.055 -10000 0 -0.2 9 9
IL1 beta fragment/IL1R1/IL1RAP 0.025 0.043 -10000 0 -0.21 14 14
NFKB1 0.022 0.017 -10000 0 -0.35 1 1
MAPK8 -0.007 0.066 0.18 35 -0.17 3 38
IRAK1 -0.026 0.045 -10000 0 -0.21 30 30
IL1RN/IL1R1 0.053 0.074 0.21 73 -0.24 9 82
IRAK4 0.023 0.003 -10000 0 -10000 0 0
PRKCI 0.021 0.007 -10000 0 -10000 0 0
TRAF6 0.022 0.005 -10000 0 -10000 0 0
PI3K 0.026 0.03 -10000 0 -0.24 5 5
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.013 0.053 -10000 0 -0.24 15 15
CHUK 0.022 0.005 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s 0.025 0.043 -10000 0 -0.21 14 14
IL1 beta/IL1R2 0.038 0.06 0.2 44 -0.23 9 53
IRAK/TRAF6/TAK1/TAB1/TAB2 0.016 0.045 -10000 0 -0.16 29 29
NF kappa B1 p50/RelA 0.029 0.048 -10000 0 -0.21 14 14
IRAK3 0.006 0.078 -10000 0 -0.35 24 24
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 0.042 0.055 -10000 0 -0.2 20 20
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.017 0.044 0.16 1 -0.2 15 16
IL1 alpha/IL1R1/IL1RAP 0.046 0.055 0.2 31 -0.23 9 40
RELA 0.022 0.004 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
SQSTM1 0.022 0.004 -10000 0 -10000 0 0
MYD88 0.022 0.004 -10000 0 -10000 0 0
IRAK/TRAF6/MEKK3 0.026 0.058 -10000 0 -0.18 30 30
IL1RAP 0.019 0.029 -10000 0 -0.35 3 3
UBE2N 0.023 0.002 -10000 0 -10000 0 0
IRAK/TRAF6 -0.024 0.053 -10000 0 -0.27 4 4
CASP1 0.021 0.023 -10000 0 -0.35 2 2
IL1RN/IL1R2 0.068 0.083 0.23 98 -0.24 3 101
IL1 beta fragment/IL1R1/IL1RAP/MYD88 0.035 0.045 -10000 0 -0.2 14 14
TMEM189-UBE2V1 -0.004 0.087 -10000 0 -0.35 31 31
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.01 0.069 -10000 0 -0.31 15 15
PIK3CA 0.02 0.018 -10000 0 -0.35 1 1
IL1RN 0.06 0.093 0.28 75 -10000 0 75
TRAF6/TAK1/TAB1/TAB2 0.027 0.05 -10000 0 -0.17 30 30
MAP2K6 0.006 0.082 0.18 56 -0.17 20 76
Regulation of nuclear SMAD2/3 signaling

Figure S84.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S84.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EP300 0.012 0.019 -10000 0 -10000 0 0
HSPA8 0.023 0.005 -10000 0 -10000 0 0
SMAD3/SMAD4/ER alpha 0.002 0.092 -10000 0 -0.23 55 55
AKT1 0.024 0.006 -10000 0 -10000 0 0
GSC 0.054 0.1 0.49 1 -0.43 4 5
NKX2-5 0.051 0.094 0.27 75 -10000 0 75
muscle cell differentiation -0.016 0.11 0.4 11 -10000 0 11
SMAD2-3/SMAD4/SP1 0.059 0.061 -10000 0 -0.24 5 5
SMAD4 0.013 0.038 -10000 0 -10000 0 0
CBFB 0.02 0.008 -10000 0 -10000 0 0
SAP18 0.022 0.005 -10000 0 -10000 0 0
Cbp/p300/MSG1 0.037 0.04 0.2 15 -0.21 3 18
SMAD3/SMAD4/VDR 0.05 0.052 0.24 2 -0.18 2 4
MYC 0.011 0.047 -10000 0 -0.35 8 8
CDKN2B -0.008 0.1 -10000 0 -0.5 12 12
AP1 -0.026 0.11 -10000 0 -0.28 25 25
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.018 0.074 -10000 0 -0.4 10 10
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 0.027 0.048 0.19 2 -0.24 4 6
SP3 0.024 0.003 -10000 0 -10000 0 0
CREB1 0.023 0.003 -10000 0 -10000 0 0
FOXH1 0.088 0.12 0.29 129 -10000 0 129
SMAD3/SMAD4/GR -0.009 0.1 -10000 0 -0.23 79 79
GATA3 0.028 0.058 0.28 13 -0.35 6 19
SKI/SIN3/HDAC complex/NCoR1 0.008 0.076 -10000 0 -0.38 13 13
MEF2C/TIF2 0.005 0.12 0.33 3 -0.36 36 39
endothelial cell migration -0.014 0.12 0.76 10 -10000 0 10
MAX 0.022 0.005 -10000 0 -10000 0 0
RBBP7 0.023 0.004 -10000 0 -10000 0 0
RBBP4 0.02 0.029 -10000 0 -0.35 3 3
RUNX2 0.029 0.045 0.28 14 -0.35 1 15
RUNX3 0.029 0.042 0.28 14 -10000 0 14
RUNX1 0.023 0.003 -10000 0 -10000 0 0
CTBP1 0.022 0.005 -10000 0 -10000 0 0
NR3C1 -0.034 0.13 -10000 0 -0.35 78 78
VDR 0.029 0.044 0.3 13 -10000 0 13
CDKN1A 0.008 0.064 -10000 0 -0.84 2 2
KAT2B 0.015 0.046 -10000 0 -0.35 8 8
SMAD2/SMAD2/SMAD4/FOXH1 0.087 0.099 0.28 47 -10000 0 47
DCP1A 0.022 0.005 -10000 0 -10000 0 0
SKI 0.023 0.004 -10000 0 -10000 0 0
SERPINE1 0.013 0.12 -10000 0 -0.77 10 10
SMAD3/SMAD4/ATF2 0.028 0.058 -10000 0 -0.29 5 5
SMAD3/SMAD4/ATF3 0.006 0.083 -10000 0 -0.24 40 40
SAP30 0.022 0.005 -10000 0 -10000 0 0
Cbp/p300/PIAS3 0.022 0.03 -10000 0 -10000 0 0
JUN -0.037 0.1 -10000 0 -0.29 23 23
SMAD3/SMAD4/IRF7 0.033 0.062 0.37 3 -0.25 3 6
TFE3 0.024 0.01 -10000 0 -10000 0 0
COL1A2 0.02 0.075 -10000 0 -0.54 7 7
mesenchymal cell differentiation -0.032 0.061 0.24 4 -0.25 11 15
DLX1 0.05 0.082 0.28 58 -10000 0 58
TCF3 0.021 0.006 -10000 0 -10000 0 0
FOS -0.086 0.17 -10000 0 -0.36 152 152
SMAD3/SMAD4/Max 0.028 0.052 -10000 0 -0.25 3 3
Cbp/p300/SNIP1 0.039 0.016 -10000 0 -10000 0 0
ZBTB17 0.02 0.01 -10000 0 -10000 0 0
LAMC1 0.006 0.042 0.21 7 -0.22 3 10
TGIF2/HDAC complex/SMAD3/SMAD4 0.028 0.052 -10000 0 -0.25 3 3
IRF7 0.028 0.038 0.29 10 -10000 0 10
ESR1 -0.017 0.11 -10000 0 -0.35 53 53
HNF4A 0.059 0.093 0.28 75 -10000 0 75
MEF2C 0.008 0.12 0.29 12 -0.36 37 49
SMAD2-3/SMAD4 0.033 0.062 -10000 0 -0.27 3 3
Cbp/p300/Src-1 0.037 0.02 -10000 0 -0.19 1 1
IGHV3OR16-13 0.006 0.032 -10000 0 -0.34 4 4
TGIF2/HDAC complex 0.022 0.005 -10000 0 -10000 0 0
CREBBP 0.014 0.017 -10000 0 -10000 0 0
SKIL 0.021 0.007 -10000 0 -10000 0 0
HDAC1 0.023 0.004 -10000 0 -10000 0 0
HDAC2 0.023 0.003 -10000 0 -10000 0 0
SNIP1 0.023 0.004 -10000 0 -10000 0 0
GCN5L2 -0.002 0.004 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 0.033 0.054 -10000 0 -0.25 3 3
MSG1/HSC70 0.037 0.038 0.21 16 -0.24 3 19
SMAD2 0.022 0.028 -10000 0 -10000 0 0
SMAD3 0.009 0.046 -10000 0 -0.37 4 4
SMAD3/E2F4-5/DP1/p107/SMAD4 0.013 0.031 -10000 0 -0.21 5 5
SMAD2/SMAD2/SMAD4 0.001 0.058 0.19 3 -0.25 12 15
NCOR1 0.021 0.007 -10000 0 -10000 0 0
NCOA2 0.009 0.064 -10000 0 -0.35 16 16
NCOA1 0.022 0.017 -10000 0 -0.35 1 1
MYOD/E2A 0.04 0.046 0.21 35 -10000 0 35
SMAD2-3/SMAD4/SP1/MIZ-1 0.067 0.062 -10000 0 -0.24 3 3
IFNB1 0.004 0.048 0.24 9 -0.23 2 11
SMAD3/SMAD4/MEF2C 0.026 0.13 0.25 3 -0.36 36 39
CITED1 0.029 0.054 0.28 17 -0.35 3 20
SMAD2-3/SMAD4/ARC105 0.043 0.062 -10000 0 -0.24 3 3
RBL1 0.022 0.005 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB 0.015 0.049 0.22 1 -0.31 4 5
RUNX1-3/PEBPB2 0.044 0.029 0.2 11 -10000 0 11
SMAD7 -0.025 0.12 -10000 0 -0.44 14 14
MYC/MIZ-1 0.02 0.038 -10000 0 -0.25 8 8
SMAD3/SMAD4 -0.011 0.068 -10000 0 -0.36 9 9
IL10 0.015 0.069 0.24 22 -0.23 4 26
PIASy/HDAC complex 0.023 0.008 -10000 0 -10000 0 0
PIAS3 0.018 0.009 -10000 0 -10000 0 0
CDK2 0.018 0.012 -10000 0 -10000 0 0
IL5 0.006 0.051 0.21 3 -0.22 6 9
CDK4 0.014 0.017 -10000 0 -10000 0 0
PIAS4 0.023 0.008 -10000 0 -10000 0 0
ATF3 -0.009 0.098 -10000 0 -0.35 39 39
SMAD3/SMAD4/SP1 0.035 0.058 -10000 0 -0.24 5 5
FOXG1 0.14 0.13 0.28 244 -10000 0 244
FOXO3 0.009 0.008 -10000 0 -10000 0 0
FOXO1 0.002 0.019 -10000 0 -0.24 2 2
FOXO4 0.002 0.019 -10000 0 -0.24 2 2
heart looping 0.008 0.12 0.29 12 -0.36 37 49
CEBPB 0.023 0.006 -10000 0 -10000 0 0
SMAD3/SMAD4/DLX1 0.043 0.073 0.23 33 -0.24 3 36
MYOD1 0.041 0.074 0.28 45 -10000 0 45
SMAD3/SMAD4/HNF4 0.05 0.08 0.22 48 -0.24 3 51
SMAD3/SMAD4/GATA3 0.037 0.07 0.25 4 -0.23 9 13
SnoN/SIN3/HDAC complex/NCoR1 0.021 0.007 -10000 0 -10000 0 0
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.057 0.052 0.27 2 -0.21 3 5
SMAD3/SMAD4/SP1-3 0.058 0.05 -10000 0 -0.21 5 5
MED15 0.022 0.005 -10000 0 -10000 0 0
SP1 0.025 0.017 -10000 0 -0.14 2 2
SIN3B 0.022 0.005 -10000 0 -10000 0 0
SIN3A 0.022 0.005 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 0.1 0.13 0.33 51 -0.21 28 79
ITGB5 0.007 0.044 0.22 5 -0.22 2 7
TGIF/SIN3/HDAC complex/CtBP 0.015 0.055 -10000 0 -0.36 6 6
SMAD3/SMAD4/AR -0.013 0.11 -10000 0 -0.22 88 88
AR -0.04 0.14 -10000 0 -0.35 87 87
negative regulation of cell growth 0.005 0.07 -10000 0 -0.29 10 10
SMAD3/SMAD4/MYOD 0.039 0.071 0.23 28 -0.25 3 31
E2F5 0.021 0.007 -10000 0 -10000 0 0
E2F4 0.02 0.008 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.09 0.093 0.28 27 -10000 0 27
SMAD2-3/SMAD4/FOXO1-3a-4 0.015 0.04 -10000 0 -0.26 4 4
TFDP1 0.022 0.006 -10000 0 -10000 0 0
SMAD3/SMAD4/AP1 -0.012 0.12 -10000 0 -0.29 23 23
SMAD3/SMAD4/RUNX2 0.032 0.061 0.25 11 -0.24 4 15
TGIF2 0.022 0.005 -10000 0 -10000 0 0
TGIF1 0.022 0.005 -10000 0 -10000 0 0
ATF2 0.021 0.028 -10000 0 -0.35 3 3
IL12-mediated signaling events

Figure S85.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S85.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IL12/IL12R/TYK2/JAK2/SOCS1 0.018 0.085 0.3 12 -0.3 9 21
TBX21 -0.021 0.25 0.67 6 -1 17 23
B2M 0.022 0.01 -10000 0 -10000 0 0
TYK2 0.013 0.031 0.17 2 -10000 0 2
IL12RB1 0.017 0.07 0.35 13 -0.38 4 17
GADD45B -0.007 0.2 0.56 7 -0.67 20 27
IL12RB2 0.029 0.071 0.28 31 -10000 0 31
GADD45G -0.022 0.26 0.56 7 -0.9 27 34
natural killer cell activation 0.001 0.02 0.15 3 -10000 0 3
RELB 0.022 0.004 -10000 0 -10000 0 0
RELA 0.022 0.004 -10000 0 -10000 0 0
IL18 0.026 0.036 0.29 8 -10000 0 8
IL2RA 0.031 0.052 0.28 20 -0.35 1 21
IFNG 0.05 0.081 0.28 57 -10000 0 57
STAT3 (dimer) -0.013 0.2 0.53 7 -0.63 23 30
HLA-DRB5 0.004 0.061 0.27 6 -0.36 9 15
FASLG 0.011 0.24 0.75 6 -0.88 15 21
NF kappa B2 p52/RelB -0.011 0.2 0.45 1 -0.81 16 17
CD4 0.008 0.027 0.23 1 -10000 0 1
SOCS1 0.021 0.017 -10000 0 -0.35 1 1
EntrezGene:6955 -0.007 0.013 -10000 0 -10000 0 0
CD3D 0.008 0.065 0.26 14 -0.35 7 21
CD3E 0.003 0.06 0.28 5 -0.36 9 14
CD3G 0.008 0.047 0.28 7 -0.36 2 9
IL12Rbeta2/JAK2 0.028 0.073 0.24 20 -0.25 9 29
CCL3 -0.009 0.22 0.72 6 -0.94 11 17
CCL4 -0.014 0.24 0.71 6 -1.1 11 17
HLA-A 0.023 0.015 0.28 1 -10000 0 1
IL18/IL18R 0.056 0.059 0.28 9 -0.22 8 17
NOS2 -0.013 0.24 0.66 6 -0.9 20 26
IL12/IL12R/TYK2/JAK2/SPHK2 0.019 0.083 0.3 12 -0.28 9 21
IL1R1 -0.023 0.25 0.64 6 -1 18 24
IL4 -0.001 0.033 -10000 0 -0.18 1 1
JAK2 0.006 0.058 0.18 1 -0.36 9 10
EntrezGene:6957 -0.006 0.012 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.016 0.13 0.29 3 -0.54 20 23
RAB7A -0.001 0.2 0.53 7 -0.63 20 27
lysosomal transport 0.001 0.19 0.53 7 -0.6 20 27
FOS -0.29 0.54 0.54 4 -1.1 164 168
STAT4 (dimer) 0.016 0.2 0.55 7 -0.62 21 28
STAT5A (dimer) 0.008 0.23 0.62 9 -0.8 17 26
GZMA -0.024 0.26 0.66 6 -1.1 17 23
GZMB -0.007 0.23 0.64 8 -1 12 20
HLX 0.019 0.008 -10000 0 -10000 0 0
LCK -0.013 0.23 0.62 7 -0.89 16 23
TCR/CD3/MHC II/CD4 -0.042 0.13 0.21 4 -0.24 118 122
IL2/IL2R 0.06 0.058 0.36 10 -0.18 3 13
MAPK14 -0.009 0.22 0.56 7 -0.69 29 36
CCR5 -0.001 0.21 0.59 7 -0.81 16 23
IL1B 0.01 0.047 0.18 1 -0.38 4 5
STAT6 0.015 0.085 0.42 6 -0.51 1 7
STAT4 0.022 0.017 -10000 0 -0.35 1 1
STAT3 0.022 0.006 -10000 0 -10000 0 0
STAT1 0.023 0.012 0.28 1 -10000 0 1
NFKB1 0.022 0.017 -10000 0 -0.35 1 1
NFKB2 0.022 0.005 -10000 0 -10000 0 0
IL12B 0.011 0.035 0.2 4 -10000 0 4
CD8A 0.018 0.055 0.29 4 -0.35 9 13
CD8B 0.03 0.071 0.28 25 -0.35 7 32
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity -0.018 0.084 0.3 9 -0.3 12 21
IL2RB 0.021 0.017 -10000 0 -0.35 1 1
proteasomal ubiquitin-dependent protein catabolic process 0.018 0.19 0.55 7 -0.57 21 28
IL2RG 0.024 0.04 0.28 6 -0.35 3 9
IL12 0.022 0.06 0.23 15 -0.26 4 19
STAT5A 0.021 0.017 -10000 0 -0.35 1 1
CD247 0.004 0.035 0.28 1 -0.35 2 3
IL2 0.026 0.045 0.28 16 -10000 0 16
SPHK2 0.023 0.004 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
IL12A 0.015 0.061 0.27 13 -0.37 4 17
IL12/IL12R/TYK2/JAK2 -0.013 0.25 0.71 7 -0.92 18 25
MAP2K3 -0.019 0.23 0.56 7 -0.66 34 41
RIPK2 0.021 0.007 -10000 0 -10000 0 0
MAP2K6 -0.004 0.22 0.56 7 -0.67 30 37
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA 0.004 0.035 -10000 0 -0.36 2 2
IL18RAP 0.021 0.042 0.3 3 -0.35 4 7
IL12Rbeta1/TYK2 0.022 0.063 0.29 12 -0.29 4 16
EOMES -0.016 0.16 -10000 0 -0.78 18 18
STAT1 (dimer) 0.018 0.2 0.62 9 -0.65 16 25
T cell proliferation 0.015 0.17 0.48 7 -0.5 21 28
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.02 0.036 -10000 0 -0.35 4 4
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.004 0.16 0.5 2 -0.53 24 26
ATF2 -0.01 0.21 0.53 7 -0.64 29 36
Retinoic acid receptors-mediated signaling

Figure S86.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S86.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.023 0.004 -10000 0 -10000 0 0
HDAC3 0.023 0.003 -10000 0 -10000 0 0
VDR 0.029 0.044 0.3 13 -10000 0 13
Cbp/p300/PCAF 0.037 0.034 -10000 0 -0.2 8 8
EP300 0.021 0.006 -10000 0 -10000 0 0
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.002 0.076 0.16 2 -0.29 22 24
KAT2B 0.017 0.046 -10000 0 -0.35 8 8
MAPK14 0.022 0.004 -10000 0 -10000 0 0
AKT1 0.003 0.07 0.26 4 -0.23 15 19
RAR alpha/9cRA/Cyclin H 0.016 0.094 -10000 0 -0.27 33 33
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA -0.004 0.087 0.16 1 -0.33 23 24
CDC2 0 0.001 -10000 0 -10000 0 0
response to UV 0 0.001 -10000 0 -10000 0 0
RAR alpha/Jnk1 0.004 0.079 -10000 0 -0.22 46 46
NCOR2 0.023 0.004 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.019 0.022 0.19 8 -10000 0 8
RXRs/RARs/NRIP1/9cRA -0.01 0.15 0.32 1 -0.46 38 39
NCOA2 0.009 0.064 -10000 0 -0.35 16 16
NCOA3 0.022 0.015 0.33 1 -10000 0 1
NCOA1 0.022 0.017 -10000 0 -0.35 1 1
VDR/VDR/DNA 0.029 0.043 0.3 13 -10000 0 13
RARG 0.023 0.004 -10000 0 -10000 0 0
RAR gamma1/9cRA 0.029 0.008 -10000 0 -10000 0 0
MAPK3 0.022 0.006 -10000 0 -10000 0 0
MAPK1 0.022 0.005 -10000 0 -10000 0 0
MAPK8 0.019 0.037 -10000 0 -0.35 5 5
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 0.009 0.13 0.28 3 -0.38 36 39
RARA 0.007 0.063 0.19 5 -0.22 29 34
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA -0.009 0.09 0.16 1 -0.32 26 27
PRKCA 0.001 0.087 -10000 0 -0.35 30 30
RXRs/RARs/NRIP1/9cRA/HDAC1 -0.011 0.16 -10000 0 -0.46 37 37
RXRG -0.014 0.12 0.23 11 -0.27 74 85
RXRA 0.005 0.06 0.19 5 -0.2 31 36
RXRB 0.011 0.08 0.23 5 -0.26 32 37
VDR/Vit D3/DNA 0.019 0.022 0.19 8 -10000 0 8
RBP1 0.008 0.072 -10000 0 -0.35 20 20
CRBP1/9-cic-RA 0.007 0.05 -10000 0 -0.24 20 20
RARB 0.017 0.049 -10000 0 -0.35 9 9
PRKCG 0.05 0.096 0.28 64 -0.35 6 70
MNAT1 0.022 0.004 -10000 0 -10000 0 0
RAR alpha/RXRs -0.012 0.14 0.27 3 -0.44 35 38
RXRs/RARs/SMRT(N-CoR2)/9cRA -0.003 0.13 0.26 3 -0.38 40 43
proteasomal ubiquitin-dependent protein catabolic process -0.004 0.11 0.21 7 -0.35 31 38
RXRs/RARs/NRIP1/9cRA/HDAC3 -0.011 0.16 -10000 0 -0.46 37 37
positive regulation of DNA binding 0.007 0.085 -10000 0 -0.26 34 34
NRIP1 -0.012 0.16 -10000 0 -0.67 16 16
RXRs/RARs -0.008 0.16 -10000 0 -0.44 40 40
RXRs/RXRs/DNA/9cRA -0.017 0.12 -10000 0 -0.38 38 38
PRKACA 0.022 0.005 -10000 0 -10000 0 0
CDK7 0.022 0.005 -10000 0 -10000 0 0
TFIIH 0.044 0.012 -10000 0 -10000 0 0
RAR alpha/9cRA 0.029 0.075 -10000 0 -0.26 14 14
CCNH 0.022 0.005 -10000 0 -10000 0 0
CREBBP 0.022 0.005 -10000 0 -10000 0 0
RAR gamma2/9cRA 0.039 0.017 -10000 0 -10000 0 0
Syndecan-3-mediated signaling events

Figure S87.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S87.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN 0.022 0.004 -10000 0 -10000 0 0
Syndecan-3/Src/Cortactin 0.011 0.099 -10000 0 -0.34 10 10
Syndecan-3/Neurocan 0.018 0.06 0.26 5 -0.36 9 14
POMC 0.026 0.071 0.28 21 -0.35 9 30
EGFR 0.014 0.06 0.33 1 -0.35 13 14
Syndecan-3/EGFR 0.011 0.063 0.3 1 -0.35 11 12
AGRP 0.019 0.014 0.28 1 -10000 0 1
NCSTN 0.019 0.009 -10000 0 -10000 0 0
PSENEN 0.022 0.005 -10000 0 -10000 0 0
RP11-540L11.1 0 0 -10000 0 -10000 0 0
APH1B 0.018 0.04 -10000 0 -0.35 6 6
APH1A 0.019 0.009 -10000 0 -10000 0 0
NCAN 0.027 0.046 0.29 15 -10000 0 15
long-term memory 0.043 0.065 -10000 0 -0.33 11 11
Syndecan-3/IL8 0.065 0.1 0.26 30 -0.35 11 41
PSEN1 0.022 0.004 -10000 0 -10000 0 0
Src/Cortactin 0.032 0.009 -10000 0 -10000 0 0
FYN 0.022 0.004 -10000 0 -10000 0 0
limb bud formation 0 0.052 -10000 0 -0.39 9 9
MC4R 0.026 0.042 0.28 14 -10000 0 14
SRC 0.022 0.005 -10000 0 -10000 0 0
PTN -0.06 0.15 -10000 0 -0.35 114 114
FGFR/FGF/Syndecan-3 0 0.052 -10000 0 -0.39 9 9
neuron projection morphogenesis -0.017 0.084 0.3 4 -0.34 8 12
Syndecan-3/AgRP 0.01 0.055 -10000 0 -0.34 11 11
Syndecan-3/AgRP/MC4R 0.041 0.069 0.27 1 -0.34 10 11
Fyn/Cortactin 0.033 0.008 -10000 0 -10000 0 0
SDC3 0 0.053 -10000 0 -0.39 9 9
GO:0007205 0 0 -10000 0 -10000 0 0
positive regulation of leukocyte migration 0.064 0.1 0.26 30 -0.34 11 41
IL8 0.097 0.12 0.28 150 -10000 0 150
Syndecan-3/Fyn/Cortactin 0.044 0.066 -10000 0 -0.33 11 11
Syndecan-3/CASK -0.001 0.052 -10000 0 -0.35 11 11
alpha-MSH/MC4R 0.036 0.06 0.22 30 -0.25 9 39
Gamma Secretase 0.045 0.04 -10000 0 -0.18 6 6
Rapid glucocorticoid signaling

Figure S88.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S88.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Gs family/GDP/Gbeta gamma 0.004 0.08 0.18 1 -0.18 79 80
MAPK9 0.005 0.001 -10000 0 -10000 0 0
adrenocorticotropin secretion -0.006 0.021 0.12 11 -10000 0 11
GNB1/GNG2 0.026 0.032 0.19 1 -0.2 9 10
GNB1 0.022 0.004 -10000 0 -10000 0 0
regulation of calcium ion transport via voltage-gated calcium channel activity 0 0 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
MAPK14 0.005 0.001 -10000 0 -10000 0 0
Gs family/GTP -0.013 0.068 -10000 0 -0.18 74 74
EntrezGene:2778 0 0 -10000 0 -10000 0 0
vasopressin secretion 0 0 -10000 0 -10000 0 0
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
glutamate secretion 0.008 0.017 0.051 74 -10000 0 74
GNAL -0.031 0.13 -10000 0 -0.35 74 74
GNG2 0.017 0.05 0.28 1 -0.35 9 10
CRH 0.022 0.039 0.28 11 -10000 0 11
mol:cortisol 0 0 -10000 0 -10000 0 0
MAPK8 0.003 0.026 -10000 0 -0.26 5 5
MAPK11 0.004 0.016 -10000 0 -0.26 2 2
IL2 signaling events mediated by PI3K

Figure S89.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S89.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.018 0.055 -10000 0 -0.34 1 1
UGCG -0.03 0.18 -10000 0 -0.64 40 40
AKT1/mTOR/p70S6K/Hsp90/TERT 0.041 0.14 0.26 8 -0.48 18 26
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucosylceramide -0.029 0.18 -10000 0 -0.62 41 41
mol:DAG 0.004 0.096 -10000 0 -0.77 7 7
CaM/Ca2+/Calcineurin A alpha-beta B1 0.013 0.15 0.26 1 -0.37 51 52
FRAP1 0.005 0.17 0.28 1 -0.42 54 55
FOXO3 0.019 0.14 0.34 6 -0.49 16 22
AKT1 0.019 0.15 0.28 1 -0.5 19 20
GAB2 0.018 0.034 -10000 0 -0.35 4 4
SMPD1 -0.009 0.14 -10000 0 -0.63 23 23
SGMS1 0.011 0.073 -10000 0 -0.58 7 7
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
mol:GDP -0.008 0.021 -10000 0 -0.21 5 5
CALM1 0.022 0.004 -10000 0 -10000 0 0
cell proliferation 0.01 0.14 0.25 4 -0.45 29 33
EIF3A 0.022 0.005 -10000 0 -10000 0 0
PI3K 0.026 0.032 -10000 0 -0.25 5 5
RPS6KB1 0.004 0.15 -10000 0 -0.81 15 15
mol:sphingomyelin 0.004 0.096 -10000 0 -0.77 7 7
natural killer cell activation 0 0.003 -10000 0 -0.013 6 6
JAK3 0.023 0.024 0.28 4 -10000 0 4
PIK3R1 0.017 0.038 -10000 0 -0.35 5 5
JAK1 0.022 0.018 -10000 0 -0.35 1 1
NFKB1 0.022 0.017 -10000 0 -0.35 1 1
MYC 0.038 0.17 0.36 9 -0.84 11 20
MYB 0.051 0.082 0.48 2 -0.78 1 3
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.024 0.095 0.24 1 -0.43 9 10
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.026 0.13 -10000 0 -0.72 15 15
mol:PI-3-4-5-P3 0.028 0.096 0.24 1 -0.42 9 10
Rac1/GDP 0.011 0.024 -10000 0 -0.18 5 5
T cell proliferation 0.027 0.095 0.23 9 -0.4 9 18
SHC1 0.018 0.011 -10000 0 -10000 0 0
RAC1 0.022 0.005 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity 0.007 0.015 0.055 48 -10000 0 48
PRKCZ 0.026 0.097 0.25 5 -0.41 9 14
NF kappa B1 p50/RelA 0.024 0.16 -10000 0 -0.39 44 44
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K 0.013 0.049 -10000 0 -0.41 3 3
HSP90AA1 0.022 0.004 -10000 0 -10000 0 0
RELA 0.022 0.004 -10000 0 -10000 0 0
IL2RA 0.029 0.053 0.28 20 -0.35 1 21
IL2RB 0.02 0.019 -10000 0 -0.35 1 1
TERT 0.12 0.13 0.28 189 -10000 0 189
E2F1 0.054 0.081 0.32 4 -0.9 1 5
SOS1 0.021 0.01 -10000 0 -10000 0 0
RPS6 0.022 0.005 -10000 0 -10000 0 0
mol:cAMP -0.004 0.008 -10000 0 -0.028 47 47
PTPN11 0.019 0.013 -10000 0 -10000 0 0
IL2RG 0.023 0.041 0.28 6 -0.35 3 9
actin cytoskeleton organization 0.027 0.095 0.23 9 -0.4 9 18
GRB2 0.02 0.011 -10000 0 -10000 0 0
IL2 0.024 0.048 0.28 16 -10000 0 16
PIK3CA 0.019 0.02 -10000 0 -0.35 1 1
Rac1/GTP 0.031 0.033 -10000 0 -0.17 5 5
LCK 0.023 0.029 0.28 4 -0.35 1 5
BCL2 -0.033 0.26 -10000 0 -0.76 54 54
PDGFR-beta signaling pathway

Figure S90.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S90.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
S1P1/Sphingosine-1-phosphate 0.014 0.091 0.26 8 -0.34 21 29
PDGFB-D/PDGFRB/SLAP 0.024 0.044 0.21 1 -0.24 12 13
PDGFB-D/PDGFRB/APS/CBL 0.036 0.044 -10000 0 -0.2 15 15
AKT1 0.013 0.098 0.32 31 -0.3 1 32
mol:PI-4-5-P2 0 0.001 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.018 0.1 0.25 14 -0.37 23 37
PIK3CA 0.02 0.018 -10000 0 -0.35 1 1
FGR -0.015 0.12 0.33 1 -0.52 21 22
mol:Ca2+ 0.008 0.11 0.24 14 -0.39 28 42
MYC 0.033 0.15 0.36 18 -0.66 12 30
SHC1 0.019 0.009 -10000 0 -10000 0 0
HRAS/GDP 0.02 0.048 0.16 20 -0.18 17 37
LRP1/PDGFRB/PDGFB 0.034 0.05 -10000 0 -0.21 19 19
GRB10 0.022 0.017 -10000 0 -0.35 1 1
PTPN11 0.023 0.003 -10000 0 -10000 0 0
GO:0007205 0.007 0.11 0.24 14 -0.39 28 42
PTEN 0.021 0.006 -10000 0 -10000 0 0
GRB2 0.022 0.006 -10000 0 -10000 0 0
GRB7 0.038 0.074 0.32 30 -0.35 2 32
PDGFB-D/PDGFRB/SHP2 0.024 0.051 -10000 0 -0.24 18 18
PDGFB-D/PDGFRB/GRB10 0.023 0.053 -10000 0 -0.24 19 19
cell cycle arrest 0.024 0.043 0.21 1 -0.24 12 13
HRAS 0.022 0.005 -10000 0 -10000 0 0
HIF1A 0.009 0.092 0.29 34 -0.27 1 35
GAB1 0.014 0.11 0.27 10 -0.37 24 34
mol:GTP 0 0 -10000 0 -10000 0 0
DNM2 0.017 0.1 0.27 24 -0.34 20 44
PDGFB-D/PDGFRB 0.036 0.043 -10000 0 -0.21 13 13
mol:GDP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.024 0.05 -10000 0 -0.24 17 17
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB 0.012 0.077 0.21 6 -0.33 14 20
positive regulation of MAPKKK cascade 0.024 0.051 -10000 0 -0.24 18 18
PIK3R1 0.018 0.037 -10000 0 -0.35 5 5
mol:IP3 0.008 0.11 0.24 14 -0.4 28 42
E5 0 0.001 -10000 0 -10000 0 0
CSK 0.02 0.009 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7 0.031 0.071 0.24 24 -0.24 21 45
SHB 0.022 0.004 -10000 0 -10000 0 0
BLK -0.017 0.14 0.38 2 -0.48 34 36
PTPN2 0.022 0.008 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 0.024 0.049 -10000 0 -0.24 17 17
BCAR1 0.02 0.007 -10000 0 -10000 0 0
VAV2 0.016 0.11 0.28 12 -0.38 24 36
CBL 0.022 0.005 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 0.023 0.052 -10000 0 -0.24 19 19
LCK -0.002 0.088 0.33 1 -0.5 9 10
PDGFRB 0.009 0.071 -10000 0 -0.35 19 19
ACP1 0.022 0.005 -10000 0 -10000 0 0
HCK 0.006 0.064 0.32 1 -0.91 1 2
ABL1 0.013 0.1 0.25 16 -0.33 24 40
PDGFB-D/PDGFRB/CBL 0.011 0.12 0.28 7 -0.41 28 35
PTPN1 0.021 0.009 -10000 0 -10000 0 0
SNX15 0.022 0.004 -10000 0 -10000 0 0
STAT3 0.022 0.006 -10000 0 -10000 0 0
STAT1 0.023 0.012 0.28 1 -10000 0 1
cell proliferation 0.034 0.14 0.35 18 -0.56 13 31
SLA 0.021 0.014 0.28 1 -10000 0 1
actin cytoskeleton reorganization -0.004 0.068 0.28 13 -0.33 1 14
SRC 0.002 0.07 0.33 1 -0.53 4 5
PI3K -0.021 0.025 -10000 0 -0.19 7 7
PDGFB-D/PDGFRB/GRB7/SHC 0.036 0.061 0.23 21 -0.2 16 37
SH2B2 0.022 0.005 -10000 0 -10000 0 0
PLCgamma1/SPHK1 0.018 0.11 0.26 13 -0.38 23 36
LYN 0.003 0.056 0.33 1 -0.44 2 3
LRP1 0.022 0.023 -10000 0 -0.35 2 2
SOS1 0.023 0.003 -10000 0 -10000 0 0
STAT5B 0.02 0.024 -10000 0 -0.35 2 2
STAT5A 0.021 0.017 -10000 0 -0.35 1 1
NCK1-2/p130 Cas 0.049 0.049 -10000 0 -0.18 13 13
SPHK1 0.023 0.019 0.3 2 -10000 0 2
EDG1 0.001 0.003 -10000 0 -10000 0 0
mol:DAG 0.008 0.11 0.24 14 -0.4 28 42
PLCG1 0.007 0.12 0.24 14 -0.4 28 42
NHERF/PDGFRB 0.036 0.046 0.2 3 -0.2 16 19
YES1 -0.006 0.086 -10000 0 -0.5 11 11
cell migration 0.036 0.046 0.2 3 -0.2 16 19
SHC/Grb2/SOS1 0.043 0.045 -10000 0 -0.18 8 8
SLC9A3R2 0.022 0.005 -10000 0 -10000 0 0
SLC9A3R1 0.023 0.02 0.28 3 -10000 0 3
NHERF1-2/PDGFRB/PTEN 0.045 0.046 0.21 3 -0.18 15 18
FYN 0.002 0.069 0.33 1 -0.61 3 4
DOK1 -0.008 0.049 0.17 23 -0.19 13 36
HRAS/GTP 0.016 0.004 -10000 0 -10000 0 0
PDGFB 0.022 0.006 -10000 0 -10000 0 0
RAC1 0.013 0.13 0.31 8 -0.45 24 32
PRKCD -0.006 0.05 0.18 26 -0.19 11 37
FER -0.007 0.05 0.18 25 -0.19 12 37
MAPKKK cascade 0.026 0.094 0.18 110 -10000 0 110
RASA1 -0.008 0.055 0.18 26 -0.2 16 42
NCK1 0.021 0.023 -10000 0 -0.35 2 2
NCK2 0.023 0.003 -10000 0 -10000 0 0
p62DOK/Csk 0.022 0.043 -10000 0 -0.18 11 11
PDGFB-D/PDGFRB/SHB 0.024 0.051 -10000 0 -0.24 18 18
chemotaxis 0.013 0.098 0.24 16 -0.32 24 40
STAT1-3-5/STAT1-3-5 0.042 0.045 -10000 0 -0.19 11 11
Bovine Papilomavirus E5/PDGFRB 0.008 0.048 -10000 0 -0.24 19 19
PTPRJ 0.022 0.004 -10000 0 -10000 0 0
ErbB2/ErbB3 signaling events

Figure S91.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S91.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
USP8 -0.007 0.009 -10000 0 -10000 0 0
RAS family/GTP 0.042 0.074 0.24 2 -0.23 6 8
NFATC4 -0.004 0.077 0.34 15 -0.2 1 16
ERBB2IP 0.02 0.009 -10000 0 -10000 0 0
HSP90 (dimer) 0.022 0.004 -10000 0 -10000 0 0
mammary gland morphogenesis 0.005 0.05 0.17 8 -0.21 9 17
JUN 0.007 0.085 0.23 6 -0.33 4 10
HRAS 0.022 0.005 -10000 0 -10000 0 0
DOCK7 -0.015 0.054 0.29 3 -0.21 7 10
ErbB2/ErbB3/neuregulin 1 beta/SHC 0.027 0.044 0.21 12 -0.2 7 19
AKT1 -0.003 0.008 -10000 0 -10000 0 0
BAD -0.008 0.005 -10000 0 -10000 0 0
MAPK10 -0.021 0.078 0.21 21 -0.18 11 32
mol:GTP 0 0.002 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta 0.007 0.058 0.22 7 -0.22 9 16
RAF1 0.036 0.088 0.26 16 -0.25 6 22
ErbB2/ErbB3/neuregulin 2 -0.002 0.08 0.2 10 -0.2 63 73
STAT3 -0.012 0.18 -10000 0 -0.78 25 25
cell migration -0.011 0.085 0.23 28 -0.2 10 38
mol:PI-3-4-5-P3 0 0.002 -10000 0 -10000 0 0
cell proliferation -0.022 0.23 0.36 5 -0.56 32 37
FOS -0.073 0.26 0.31 7 -0.44 160 167
NRAS 0.023 0.002 -10000 0 -10000 0 0
mol:Ca2+ 0.005 0.05 0.17 8 -0.21 9 17
MAPK3 0.002 0.19 0.35 7 -0.57 24 31
MAPK1 -0.003 0.2 0.34 5 -0.6 23 28
JAK2 -0.018 0.053 0.36 2 -0.21 5 7
NF2 0.005 0.029 -10000 0 -0.64 1 1
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 0.01 0.041 0.19 4 -0.22 8 12
NRG1 0.014 0.048 0.28 1 -0.35 8 9
GRB2/SOS1 0.032 0.01 -10000 0 -10000 0 0
MAPK8 -0.001 0.067 0.26 5 -0.24 13 18
MAPK9 0 0.063 0.22 23 -10000 0 23
ERBB2 -0.008 0.057 0.32 14 -10000 0 14
ERBB3 0.02 0.029 -10000 0 -0.35 3 3
SHC1 0.019 0.009 -10000 0 -10000 0 0
RAC1 0.022 0.005 -10000 0 -10000 0 0
apoptosis 0.007 0.008 -10000 0 -10000 0 0
STAT3 (dimer) -0.012 0.17 -10000 0 -0.76 26 26
RNF41 -0.01 0.008 -10000 0 -10000 0 0
FRAP1 -0.003 0.005 -10000 0 -10000 0 0
RAC1-CDC42/GTP -0.017 0.03 -10000 0 -0.16 8 8
ErbB2/ErbB2/HSP90 (dimer) -0.009 0.036 0.21 12 -10000 0 12
CHRNA1 0.027 0.16 0.28 32 -0.37 20 52
myelination 0.013 0.1 0.31 37 -10000 0 37
PPP3CB -0.015 0.048 0.43 1 -0.2 7 8
KRAS 0.023 0.014 0.33 1 -10000 0 1
RAC1-CDC42/GDP 0.044 0.056 0.22 6 -0.2 7 13
NRG2 -0.027 0.12 -10000 0 -0.35 68 68
mol:GDP 0.01 0.04 0.18 4 -0.22 8 12
SOS1 0.023 0.004 -10000 0 -10000 0 0
MAP2K2 0.029 0.093 0.21 41 -0.28 5 46
SRC 0.022 0.005 -10000 0 -10000 0 0
mol:cAMP -0.001 0.001 -10000 0 -10000 0 0
PTPN11 -0.015 0.053 0.29 3 -0.2 9 12
MAP2K1 -0.006 0.19 0.44 1 -0.56 24 25
heart morphogenesis 0.005 0.05 0.17 8 -0.21 9 17
RAS family/GDP 0.048 0.069 0.25 3 -0.22 6 9
GRB2 0.022 0.006 -10000 0 -10000 0 0
PRKACA 0.008 0.039 -10000 0 -0.61 2 2
CHRNE 0.006 0.025 0.084 3 -0.16 4 7
HSP90AA1 0.022 0.004 -10000 0 -10000 0 0
activation of caspase activity 0.003 0.008 -10000 0 -10000 0 0
nervous system development 0.005 0.05 0.17 8 -0.21 9 17
CDC42 0.022 0.004 -10000 0 -10000 0 0
Sphingosine 1-phosphate (S1P) pathway

Figure S92.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S92.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.023 0.004 -10000 0 -10000 0 0
SPHK1 0.023 0.018 0.3 2 -10000 0 2
GNAI2 0.022 0.005 -10000 0 -10000 0 0
mol:S1P 0.01 0.005 -10000 0 -10000 0 0
GNAO1 -0.065 0.16 -10000 0 -0.35 120 120
mol:Sphinganine-1-P -0.01 0.015 0.2 2 -10000 0 2
growth factor activity 0 0 -10000 0 -10000 0 0
S1P/S1P2/G12/G13 0.041 0.037 -10000 0 -0.19 5 5
GNAI3 0.023 0.002 -10000 0 -10000 0 0
G12/G13 0.031 0.01 -10000 0 -10000 0 0
S1PR3 0.01 0.066 -10000 0 -0.35 17 17
S1PR2 0.021 0.006 -10000 0 -10000 0 0
EDG1 0 0 -10000 0 -10000 0 0
S1P1/S1P 0.001 0.03 -10000 0 -0.22 5 5
S1PR5 0.025 0.053 0.29 13 -0.35 4 17
S1PR4 0.02 0.026 0.28 1 -0.35 2 3
GNAI1 0.017 0.046 -10000 0 -0.35 8 8
S1P/S1P5/G12 0.034 0.044 0.2 8 -0.2 7 15
S1P/S1P3/Gq -0.015 0.11 -10000 0 -0.31 53 53
S1P/S1P4/Gi -0.038 0.11 -10000 0 -0.22 113 113
GNAQ 0.021 0.017 -10000 0 -0.35 1 1
GNAZ 0.011 0.062 -10000 0 -0.35 15 15
GNA14 -0.01 0.1 -10000 0 -0.35 44 44
GNA15 0.025 0.03 0.28 7 -10000 0 7
GNA12 0.022 0.005 -10000 0 -10000 0 0
GNA13 0.022 0.005 -10000 0 -10000 0 0
GNA11 0.015 0.049 -10000 0 -0.35 9 9
ABCC1 0.022 0.005 -10000 0 -10000 0 0
Insulin-mediated glucose transport

Figure S93.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S93.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Insulin responsive Vesicles -0.067 0.13 -10000 0 -0.37 33 33
CaM/Ca2+ 0.017 0.003 -10000 0 -10000 0 0
AKT1 0.022 0.004 -10000 0 -10000 0 0
AKT2 0.022 0.005 -10000 0 -10000 0 0
STXBP4 0.022 0.005 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucose -0.075 0.14 0.3 1 -0.39 36 37
YWHAZ 0.021 0.007 -10000 0 -10000 0 0
CALM1 0.022 0.004 -10000 0 -10000 0 0
YWHAQ 0.022 0.005 -10000 0 -10000 0 0
TBC1D4 -0.012 0.015 -10000 0 -0.25 2 2
mol:Ca2+ 0 0 -10000 0 -10000 0 0
YWHAH 0.022 0.006 -10000 0 -10000 0 0
YWHAB 0.022 0.005 -10000 0 -10000 0 0
SNARE/Synip 0.04 0.016 -10000 0 -10000 0 0
YWHAG 0.022 0.004 -10000 0 -10000 0 0
ASIP 0.02 0.013 0.28 1 -10000 0 1
PRKCI 0.021 0.007 -10000 0 -10000 0 0
AS160/CaM/Ca2+ 0.017 0.003 -10000 0 -10000 0 0
RHOQ 0.023 0.003 -10000 0 -10000 0 0
GYS1 0.006 0.015 0.24 2 -10000 0 2
PRKCZ 0.022 0.02 0.28 1 -0.35 1 2
TRIP10 0.021 0.006 -10000 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0.029 0.009 -10000 0 -10000 0 0
AS160/14-3-3 0.052 0.053 0.22 8 -0.25 5 13
VAMP2 0.021 0.007 -10000 0 -10000 0 0
SLC2A4 -0.083 0.15 0.31 1 -0.44 36 37
STX4 0.022 0.005 -10000 0 -10000 0 0
GSK3B 0.014 0.005 -10000 0 -10000 0 0
SFN 0.21 0.12 0.28 372 -10000 0 372
LNPEP 0.022 0.004 -10000 0 -10000 0 0
YWHAE 0.021 0.007 -10000 0 -10000 0 0
FoxO family signaling

Figure S94.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S94.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
G6PC 0.005 0.048 -10000 0 -10000 0 0
PLK1 0.14 0.19 0.44 21 -0.61 5 26
CDKN1B 0.06 0.17 0.36 9 -0.4 34 43
FOXO3 0.1 0.19 0.41 20 -0.46 21 41
KAT2B 0.027 0.057 -10000 0 -0.34 8 8
FOXO1/SIRT1 0.013 0.046 0.25 1 -10000 0 1
CAT 0.093 0.18 0.46 9 -0.65 5 14
CTNNB1 0.022 0.004 -10000 0 -10000 0 0
AKT1 0.035 0.033 -10000 0 -10000 0 0
FOXO1 0.008 0.051 0.27 3 -10000 0 3
MAPK10 -0.016 0.081 0.2 11 -0.17 104 115
mol:GTP 0.001 0.001 -10000 0 -10000 0 0
FOXO4 0.007 0.081 0.3 3 -0.29 6 9
response to oxidative stress 0.017 0.024 -10000 0 -10000 0 0
FOXO3A/SIRT1 0.083 0.17 0.36 16 -0.44 21 37
XPO1 0.023 0.003 -10000 0 -10000 0 0
EP300 0.022 0.006 -10000 0 -10000 0 0
BCL2L11 0.038 0.086 -10000 0 -0.74 5 5
FOXO1/SKP2 0.019 0.047 0.28 1 -10000 0 1
mol:GDP 0.017 0.024 -10000 0 -10000 0 0
RAN 0.023 0.003 -10000 0 -10000 0 0
GADD45A 0.071 0.12 0.36 1 -0.58 3 4
YWHAQ 0.022 0.005 -10000 0 -10000 0 0
FOXO1/14-3-3 family 0.032 0.15 0.24 5 -0.49 29 34
MST1 0.035 0.042 0.3 5 -10000 0 5
CSNK1D 0.022 0.006 -10000 0 -10000 0 0
CSNK1E 0.021 0.006 -10000 0 -10000 0 0
FOXO4/14-3-3 family 0.05 0.12 0.24 1 -0.42 24 25
YWHAB 0.022 0.005 -10000 0 -10000 0 0
MAPK8 0.018 0.035 0.21 9 -0.16 5 14
MAPK9 0.02 0.033 0.2 12 -10000 0 12
YWHAG 0.022 0.004 -10000 0 -10000 0 0
YWHAE 0.021 0.007 -10000 0 -10000 0 0
YWHAZ 0.021 0.007 -10000 0 -10000 0 0
SIRT1 0.012 0.027 -10000 0 -0.35 2 2
SOD2 0.078 0.14 0.43 6 -0.46 6 12
RBL2 0.031 0.26 0.45 1 -0.68 43 44
RAL/GDP 0.04 0.025 -10000 0 -10000 0 0
CHUK 0.033 0.032 -10000 0 -10000 0 0
Ran/GTP 0.018 0.003 -10000 0 -10000 0 0
CSNK1G2 0.021 0.006 -10000 0 -10000 0 0
RAL/GTP 0.041 0.025 -10000 0 -10000 0 0
CSNK1G1 0.022 0.005 -10000 0 -10000 0 0
FASLG 0.038 0.12 -10000 0 -1.2 4 4
SKP2 0.022 0.005 -10000 0 -10000 0 0
USP7 0.023 0.005 -10000 0 -10000 0 0
IKBKB 0.029 0.033 -10000 0 -10000 0 0
CCNB1 0.1 0.18 0.43 17 -0.58 6 23
FOXO1-3a-4/beta catenin 0.07 0.12 0.37 9 -0.37 5 14
proteasomal ubiquitin-dependent protein catabolic process 0.019 0.047 0.28 1 -10000 0 1
CSNK1A1 0.022 0.004 -10000 0 -10000 0 0
SGK1 0.033 0.037 -10000 0 -0.37 1 1
CSNK1G3 0.022 0.004 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.033 0.007 -10000 0 -10000 0 0
ZFAND5 0.007 0.072 0.32 1 -0.33 1 2
SFN 0.21 0.12 0.28 372 -10000 0 372
CDK2 0.022 0.005 -10000 0 -10000 0 0
FOXO3A/14-3-3 0.069 0.12 0.23 9 -0.42 19 28
CREBBP 0.022 0.006 -10000 0 -10000 0 0
FBXO32 0.022 0.4 0.51 29 -0.96 67 96
BCL6 0.086 0.16 0.45 1 -0.59 8 9
RALB 0.023 0.003 -10000 0 -10000 0 0
RALA 0.023 0.004 -10000 0 -10000 0 0
YWHAH 0.022 0.006 -10000 0 -10000 0 0
Regulation of Telomerase

Figure S95.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S95.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Telomerase catalytic core complex 0.003 0.12 -10000 0 -0.57 1 1
RAD9A 0.022 0.004 -10000 0 -10000 0 0
AP1 -0.046 0.13 -10000 0 -0.25 154 154
IFNAR2 0.027 0.018 -10000 0 -0.34 1 1
AKT1 0.009 0.061 0.23 2 -0.33 3 5
ER alpha/Oestrogen -0.007 0.079 -10000 0 -0.24 54 54
NFX1/SIN3/HDAC complex 0.017 0.06 -10000 0 -0.35 9 9
EGF 0.033 0.052 0.28 20 -0.34 1 21
SMG5 0.019 0.009 -10000 0 -10000 0 0
SMG6 0.021 0.006 -10000 0 -10000 0 0
SP3/HDAC2 0.042 0.013 -10000 0 -10000 0 0
TERT/c-Abl 0.003 0.12 -10000 0 -0.57 1 1
SAP18 0.023 0.005 -10000 0 -10000 0 0
MRN complex 0.041 0.016 -10000 0 -10000 0 0
WT1 -0.24 0.17 -10000 0 -0.35 372 372
WRN 0.02 0.008 -10000 0 -10000 0 0
SP1 0.03 0.01 -10000 0 -10000 0 0
SP3 0.025 0.004 -10000 0 -10000 0 0
TERF2IP 0.02 0.008 -10000 0 -10000 0 0
Telomerase/Nucleolin 0.002 0.11 -10000 0 -0.51 1 1
Mad/Max 0.039 0.012 -10000 0 -10000 0 0
TERT 0.003 0.12 -10000 0 -0.58 1 1
CCND1 0.005 0.12 -10000 0 -0.5 1 1
MAX 0.025 0.005 -10000 0 -10000 0 0
RBBP7 0.024 0.004 -10000 0 -10000 0 0
RBBP4 0.021 0.029 -10000 0 -0.35 3 3
TERF2 0.018 0.01 -10000 0 -10000 0 0
PTGES3 0.023 0.003 -10000 0 -10000 0 0
SIN3A 0.023 0.005 -10000 0 -10000 0 0
Telomerase/911 0.025 0.042 -10000 0 -0.36 1 1
CDKN1B -0.002 0.1 -10000 0 -0.46 23 23
RAD1 0.022 0.004 -10000 0 -10000 0 0
XRCC5 0.023 0.003 -10000 0 -10000 0 0
XRCC6 0.022 0.006 -10000 0 -10000 0 0
SAP30 0.023 0.005 -10000 0 -10000 0 0
TRF2/PARP2 0.029 0.013 -10000 0 -10000 0 0
UBE3A 0.024 0.006 -10000 0 -10000 0 0
JUN 0.02 0.043 -10000 0 -0.35 7 7
E6 0.002 0.003 -10000 0 -10000 0 0
HPV-16 E6/E6AP 0.022 0.008 -10000 0 -10000 0 0
FOS -0.084 0.17 -10000 0 -0.35 152 152
IFN-gamma/IRF1 0.049 0.085 0.22 57 -0.25 23 80
PARP2 0.022 0.004 -10000 0 -10000 0 0
BLM 0.051 0.082 0.28 58 -10000 0 58
Telomerase 0.027 0.086 0.22 6 -0.43 7 13
IRF1 0.019 0.037 -10000 0 -0.15 23 23
ESR1 -0.016 0.11 -10000 0 -0.35 54 54
KU/TER 0.032 0.009 -10000 0 -10000 0 0
ATM/TRF2 0.03 0.012 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.021 0.059 -10000 0 -0.3 11 11
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.021 0.06 -10000 0 -0.31 11 11
HDAC1 0.023 0.004 -10000 0 -10000 0 0
HDAC2 0.029 0.008 -10000 0 -10000 0 0
ATM 0.015 0.019 -10000 0 -10000 0 0
SMAD3 -0.016 0.021 -10000 0 -0.25 4 4
ABL1 0.02 0.024 -10000 0 -0.35 2 2
MXD1 0.025 0.005 -10000 0 -10000 0 0
MRE11A 0.022 0.004 -10000 0 -10000 0 0
HUS1 0.023 0.004 -10000 0 -10000 0 0
RPS6KB1 0.022 0.005 -10000 0 -10000 0 0
TERT/NF kappa B1/14-3-3 0.022 0.12 -10000 0 -0.53 1 1
NR2F2 -0.011 0.078 -10000 0 -0.35 24 24
MAPK3 0.002 0.024 0.11 16 -10000 0 16
MAPK1 0.002 0.024 0.11 15 -10000 0 15
TGFB1/TGF beta receptor Type II 0.02 0.017 -10000 0 -0.35 1 1
NFKB1 0.022 0.017 -10000 0 -0.35 1 1
HNRNPC 0.022 0.004 -10000 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0.015 0.019 -10000 0 -10000 0 0
NBN 0.021 0.007 -10000 0 -10000 0 0
EGFR 0.016 0.06 0.33 1 -0.35 13 14
mol:Oestrogen 0.001 0.002 -10000 0 -10000 0 0
EGF/EGFR 0.036 0.057 0.21 20 -0.24 13 33
MYC 0.016 0.047 -10000 0 -0.35 8 8
IL2 0.034 0.046 0.29 16 -10000 0 16
KU 0.032 0.009 -10000 0 -10000 0 0
RAD50 0.023 0.003 -10000 0 -10000 0 0
HSP90AA1 0.022 0.004 -10000 0 -10000 0 0
TGFB1 0.02 0.017 -10000 0 -0.35 1 1
TRF2/BLM 0.044 0.051 0.2 47 -10000 0 47
FRAP1 0 0 -10000 0 -10000 0 0
KU/TERT 0.01 0.12 -10000 0 -0.53 1 1
SP1/HDAC2 0.048 0.02 -10000 0 -10000 0 0
PINX1 0.02 0.008 -10000 0 -10000 0 0
Telomerase/EST1A -0.001 0.11 -10000 0 -0.51 1 1
Smad3/Myc 0.003 0.036 -10000 0 -0.23 9 9
911 complex 0.043 0.013 -10000 0 -10000 0 0
IFNG 0.046 0.091 0.28 57 -0.15 23 80
Telomerase/PinX1 -0.003 0.11 -10000 0 -0.51 1 1
Telomerase/AKT1/mTOR/p70S6K 0.018 0.076 0.27 3 -0.37 9 12
SIN3B 0.023 0.006 -10000 0 -10000 0 0
YWHAE 0.021 0.007 -10000 0 -10000 0 0
Telomerase/EST1B 0.002 0.1 -10000 0 -0.51 1 1
response to DNA damage stimulus 0.004 0.019 -10000 0 -10000 0 0
MRN complex/TRF2/Rap1 0.052 0.027 -10000 0 -10000 0 0
TRF2/WRN 0.027 0.015 -10000 0 -10000 0 0
Telomerase/hnRNP C1/C2 0.001 0.11 -10000 0 -0.51 1 1
E2F1 0.077 0.1 0.29 98 -10000 0 98
ZNFX1 0.023 0.005 -10000 0 -10000 0 0
PIF1 0.086 0.11 0.28 129 -10000 0 129
NCL 0.023 0.003 -10000 0 -10000 0 0
DKC1 0.023 0.003 -10000 0 -10000 0 0
telomeric DNA binding 0 0 -10000 0 -10000 0 0
IL23-mediated signaling events

Figure S96.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S96.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CCL2 0.19 0.26 0.65 10 -1.1 8 18
IL23A 0.2 0.25 0.71 10 -1.2 4 14
NF kappa B1 p50/RelA/I kappa B alpha 0.18 0.22 0.58 3 -1.1 5 8
positive regulation of T cell mediated cytotoxicity 0.21 0.26 0.66 21 -1.2 5 26
ITGA3 0.19 0.24 0.66 8 -1.1 5 13
IL17F 0.15 0.19 0.5 29 -0.68 5 34
IL12B 0.063 0.049 0.19 14 -10000 0 14
STAT1 (dimer) 0.19 0.24 0.61 8 -1.1 5 13
CD4 0.2 0.23 0.64 10 -1 5 15
IL23 0.19 0.24 0.67 8 -1.2 4 12
IL23R 0.1 0.098 0.45 1 -0.58 2 3
IL1B 0.2 0.25 0.7 10 -1.1 8 18
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 0.22 0.25 0.68 19 -1.1 4 23
TYK2 0.044 0.034 -10000 0 -10000 0 0
STAT4 0.022 0.017 -10000 0 -0.35 1 1
STAT3 0.022 0.006 -10000 0 -10000 0 0
IL18RAP 0.022 0.039 0.29 3 -0.35 4 7
IL12RB1 0.049 0.068 0.35 13 -0.37 4 17
PIK3CA 0.02 0.018 -10000 0 -0.35 1 1
IL12Rbeta1/TYK2 0.057 0.059 0.28 12 -0.27 4 16
IL23R/JAK2 0.13 0.12 0.47 1 -0.48 1 2
positive regulation of chronic inflammatory response 0.21 0.26 0.66 21 -1.2 5 26
natural killer cell activation -0.007 0.008 -10000 0 -0.042 2 2
JAK2 0.057 0.072 0.2 4 -0.35 9 13
PIK3R1 0.018 0.037 -10000 0 -0.35 5 5
NFKB1 0.026 0.018 -10000 0 -0.35 1 1
RELA 0.026 0.008 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation 0.19 0.23 0.66 8 -1.1 4 12
ALOX12B 0.19 0.23 0.66 8 -1.1 4 12
CXCL1 0.2 0.28 0.67 17 -1.1 12 29
T cell proliferation 0.21 0.26 0.66 21 -1.2 5 26
NFKBIA 0.026 0.008 -10000 0 -10000 0 0
IL17A 0.15 0.17 0.44 40 -0.52 5 45
PI3K 0.16 0.23 0.58 3 -1.1 5 8
IFNG 0.027 0.038 0.11 46 -0.11 2 48
STAT3 (dimer) 0.16 0.22 0.56 4 -1 5 9
IL18R1 0.021 0.033 -10000 0 -0.35 4 4
IL23/IL23R/JAK2/TYK2/SOCS3 0.17 0.2 0.53 26 -0.75 5 31
IL18/IL18R 0.048 0.049 0.26 10 -0.21 8 18
macrophage activation 0.012 0.017 0.042 62 -0.044 4 66
TNF 0.2 0.25 0.67 16 -1.2 5 21
STAT3/STAT4 0.18 0.23 0.59 6 -1.1 5 11
STAT4 (dimer) 0.19 0.24 0.62 7 -1.1 5 12
IL18 0.027 0.033 0.29 8 -10000 0 8
IL19 0.23 0.25 0.66 24 -1 5 29
STAT5A (dimer) 0.18 0.24 0.62 7 -1.2 5 12
STAT1 0.023 0.012 0.28 1 -10000 0 1
SOCS3 0.021 0.024 -10000 0 -0.35 2 2
CXCL9 0.2 0.27 0.66 18 -1.1 8 26
MPO 0.19 0.24 0.65 11 -1 5 16
positive regulation of humoral immune response 0.21 0.26 0.66 21 -1.2 5 26
IL23/IL23R/JAK2/TYK2 0.21 0.26 0.66 21 -1.2 5 26
IL6 0.18 0.29 0.66 11 -1 18 29
STAT5A 0.021 0.017 -10000 0 -0.35 1 1
IL2 0.008 0.055 0.28 16 -10000 0 16
positive regulation of tyrosine phosphorylation of STAT protein -0.007 0.008 -10000 0 -0.042 2 2
CD3E 0.18 0.28 0.64 13 -1.1 12 25
keratinocyte proliferation 0.21 0.26 0.66 21 -1.2 5 26
NOS2 0.18 0.27 0.65 11 -0.99 12 23
JNK signaling in the CD4+ TCR pathway

Figure S97.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S97.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
LAT/GRAP2/SLP76/HPK1 0.048 0.051 0.23 10 -0.19 14 24
MAP4K1 0.028 0.041 0.29 12 -10000 0 12
MAP3K8 0.02 0.029 -10000 0 -0.35 3 3
PRKCB 0 0.088 -10000 0 -0.35 31 31
DBNL 0.023 0.004 -10000 0 -10000 0 0
CRKL 0.022 0.005 -10000 0 -10000 0 0
MAP3K1 0.007 0.045 -10000 0 -0.26 3 3
JUN -0.045 0.19 -10000 0 -0.56 59 59
MAP3K7 0.005 0.047 -10000 0 -0.26 3 3
GRAP2 0.011 0.062 -10000 0 -0.35 15 15
CRK 0.021 0.006 -10000 0 -10000 0 0
MAP2K4 0.004 0.061 -10000 0 -0.25 14 14
LAT 0.022 0.005 -10000 0 -10000 0 0
LCP2 0.023 0.012 0.28 1 -10000 0 1
MAPK8 -0.042 0.2 -10000 0 -0.58 59 59
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family 0.014 0.049 -10000 0 -0.2 11 11
LAT/GRAP2/SLP76/HPK1/HIP-55 0.056 0.049 0.27 3 -0.18 11 14
Ceramide signaling pathway

Figure S98.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S98.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 -0.011 0.011 -10000 0 -0.24 1 1
MAP4K4 0.006 0.057 0.21 4 -0.28 7 11
BAG4 0.019 0.024 -10000 0 -0.35 2 2
PKC zeta/ceramide 0.013 0.041 0.2 1 -0.19 17 18
NFKBIA 0.022 0.004 -10000 0 -10000 0 0
BIRC3 0.018 0.046 0.28 2 -0.35 7 9
BAX 0.005 0.045 -10000 0 -0.33 8 8
RIPK1 0.022 0.004 -10000 0 -10000 0 0
AKT1 0.001 0.087 0.66 9 -10000 0 9
BAD -0.001 0.045 0.2 10 -0.18 18 28
SMPD1 0.011 0.058 0.16 21 -0.23 13 34
RB1 -0.004 0.035 0.2 1 -0.18 18 19
FADD/Caspase 8 0.01 0.067 0.22 8 -0.31 10 18
MAP2K4 -0.006 0.038 0.18 5 -0.17 19 24
NSMAF 0.021 0.007 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.003 0.047 0.2 12 -0.17 20 32
EGF 0.031 0.052 0.28 20 -0.35 1 21
mol:ceramide -0.001 0.037 0.12 1 -0.19 18 19
MADD 0.022 0.005 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid -0.01 0.011 -10000 0 -0.24 1 1
ASAH1 0.02 0.008 -10000 0 -10000 0 0
negative regulation of cell cycle -0.004 0.035 0.2 1 -0.18 18 19
cell proliferation -0.014 0.075 0.18 3 -0.21 19 22
BID -0.013 0.17 -10000 0 -0.62 32 32
MAP3K1 -0.004 0.037 0.17 3 -0.18 18 21
EIF2A 0.002 0.054 0.18 33 -0.18 12 45
TRADD 0.02 0.008 -10000 0 -10000 0 0
CRADD 0.023 0.002 -10000 0 -10000 0 0
MAPK3 -0.004 0.048 0.2 11 -0.18 14 25
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.007 0.052 0.19 12 -0.18 14 26
Cathepsin D/ceramide 0.014 0.038 0.18 1 -0.18 17 18
FADD 0.006 0.06 0.21 6 -0.28 8 14
KSR1 -0.003 0.043 0.2 7 -0.18 20 27
MAPK8 -0.003 0.051 -10000 0 -0.22 8 8
PRKRA -0.002 0.039 0.19 5 -0.18 17 22
PDGFA 0.021 0.017 -10000 0 -0.35 1 1
TRAF2 0.022 0.006 -10000 0 -10000 0 0
IGF1 -0.048 0.15 -10000 0 -0.35 99 99
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.001 0.037 0.12 1 -0.19 18 19
CTSD 0.022 0.012 0.28 1 -10000 0 1
regulation of nitric oxide biosynthetic process 0.032 0.015 -10000 0 -0.24 1 1
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.013 0.08 0.19 3 -0.22 18 21
PRKCD 0.022 0.005 -10000 0 -10000 0 0
PRKCZ 0.022 0.02 0.28 1 -0.35 1 2
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine -0.01 0.011 -10000 0 -0.24 1 1
RelA/NF kappa B1 0.032 0.015 -10000 0 -0.24 1 1
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.023 0.002 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD 0.011 0.052 0.23 1 -0.38 2 3
TNFR1A/BAG4/TNF-alpha 0.054 0.054 0.2 50 -0.21 2 52
mol:Sphingosine-1-phosphate -0.011 0.011 -10000 0 -0.24 1 1
MAP2K1 -0.006 0.046 0.19 13 -0.17 19 32
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.022 0.004 -10000 0 -10000 0 0
CYCS 0.016 0.05 0.16 16 -0.16 4 20
TNFRSF1A 0.022 0.004 -10000 0 -10000 0 0
NFKB1 0.022 0.017 -10000 0 -0.35 1 1
TNFR1A/BAG4 0.029 0.021 -10000 0 -0.24 2 2
EIF2AK2 -0.003 0.042 0.2 10 -0.18 15 25
TNF-alpha/TNFR1A/FAN 0.056 0.053 0.2 51 -0.21 1 52
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.018 0.059 -10000 0 -0.36 7 7
MAP2K2 -0.006 0.046 0.19 12 -0.17 20 32
SMPD3 0.003 0.088 0.19 7 -0.27 38 45
TNF 0.053 0.089 0.28 64 -0.35 2 66
PKC zeta/PAR4 0.033 0.016 0.21 1 -0.24 1 2
mol:PHOSPHOCHOLINE -0.002 0.035 0.13 3 -0.14 9 12
NF kappa B1/RelA/I kappa B alpha 0.06 0.027 -10000 0 -0.18 2 2
AIFM1 0.015 0.051 0.16 15 -0.16 4 19
BCL2 -0.01 0.1 -10000 0 -0.35 44 44
HIV-1 Nef: Negative effector of Fas and TNF-alpha

Figure S99.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S99.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BAG4 0.019 0.024 -10000 0 -0.35 2 2
Caspase 8 (4 units) 0.029 0.048 -10000 0 -0.59 1 1
NEF 0.001 0.019 -10000 0 -0.2 4 4
NFKBIA 0.022 0.014 -10000 0 -10000 0 0
BIRC3 0.01 0.057 0.2 2 -0.4 7 9
CYCS 0.024 0.067 0.17 68 -0.62 1 69
RIPK1 0.022 0.004 -10000 0 -10000 0 0
CD247 0.02 0.031 0.33 1 -0.25 4 5
MAP2K7 0.005 0.19 0.29 2 -0.67 31 33
protein ubiquitination 0.011 0.077 0.28 7 -0.28 9 16
CRADD 0.023 0.002 -10000 0 -10000 0 0
DAXX 0.023 0.004 -10000 0 -10000 0 0
FAS 0.019 0.033 -10000 0 -0.35 4 4
BID 0.029 0.069 0.18 69 -0.25 6 75
NF-kappa-B/RelA/I kappa B alpha 0.043 0.037 -10000 0 -0.22 8 8
TRADD 0.02 0.008 -10000 0 -10000 0 0
MAP3K5 0.022 0.017 -10000 0 -0.35 1 1
CFLAR 0.023 0.003 -10000 0 -10000 0 0
FADD 0.022 0.004 -10000 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin 0.043 0.038 -10000 0 -0.23 8 8
MAPK8 0.007 0.18 0.36 7 -0.62 31 38
APAF1 0.023 0.002 -10000 0 -10000 0 0
TRAF1 0.022 0.005 -10000 0 -10000 0 0
TRAF2 0.022 0.006 -10000 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG 0.036 0.072 0.19 69 -0.26 6 75
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0.003 0.09 0.21 3 -0.33 17 20
CHUK 0.011 0.079 0.29 7 -0.31 8 15
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.057 0.033 -10000 0 -0.18 5 5
TCRz/NEF 0.017 0.03 0.16 7 -0.24 4 11
TNF 0.053 0.089 0.28 64 -0.35 2 66
FASLG 0.012 0.046 0.25 8 -0.33 4 12
NFKB1 0.021 0.021 -10000 0 -0.35 1 1
TNFR1A/BAG4/TNF-alpha 0.054 0.054 0.2 50 -0.21 2 52
CASP6 0.041 0.1 -10000 0 -0.46 14 14
CASP7 0.031 0.1 0.37 8 -0.43 9 17
RELA 0.022 0.014 -10000 0 -10000 0 0
CASP2 0.022 0.005 -10000 0 -10000 0 0
CASP3 0.03 0.11 0.38 9 -0.43 10 19
TNFRSF1A 0.022 0.004 -10000 0 -10000 0 0
TNFR1A/BAG4 0.029 0.021 -10000 0 -0.24 2 2
CASP8 0.023 0.003 -10000 0 -10000 0 0
CASP9 0.022 0.005 -10000 0 -10000 0 0
MAP3K14 0.009 0.083 0.21 2 -0.32 13 15
APAF-1/Caspase 9 0.028 0.059 -10000 0 -0.29 7 7
BCL2 -0.005 0.17 0.34 6 -0.58 30 36
Signaling events mediated by PRL

Figure S100.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S100.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CCNE1 0.13 0.13 0.29 211 -10000 0 211
mol:Halofuginone 0.002 0 -10000 0 -10000 0 0
ITGA1 0.021 0.023 -10000 0 -0.35 2 2
CDKN1A 0.002 0.043 -10000 0 -0.31 6 6
PRL-3/alpha Tubulin 0.031 0.011 -10000 0 -10000 0 0
mol:Ca2+ -0.037 0.077 0.28 2 -0.25 54 56
AGT -0.023 0.13 0.29 8 -0.35 65 73
CCNA2 -0.021 0.056 0.21 5 -10000 0 5
TUBA1B 0.023 0.002 -10000 0 -10000 0 0
EGR1 -0.021 0.081 -10000 0 -0.24 65 65
CDK2/Cyclin E1 0.091 0.1 0.29 18 -0.27 9 27
MAPK3 -0.01 0.004 -10000 0 -10000 0 0
PRL-2 /Rab GGTase beta 0.033 0.006 -10000 0 -10000 0 0
MAPK1 -0.01 0.004 -10000 0 -10000 0 0
PTP4A1 -0.027 0.055 -10000 0 -10000 0 0
PTP4A3 0.021 0.007 -10000 0 -10000 0 0
PTP4A2 0.022 0.004 -10000 0 -10000 0 0
ITGB1 -0.01 0.004 -10000 0 -10000 0 0
SRC 0.022 0.005 -10000 0 -10000 0 0
RAC1 0 0.047 -10000 0 -0.33 7 7
Rab GGTase beta/Rab GGTase alpha 0.033 0.007 -10000 0 -10000 0 0
PRL-1/ATF-5 0 0.071 0.35 1 -10000 0 1
RABGGTA 0.022 0.004 -10000 0 -10000 0 0
BCAR1 -0.016 0.008 -10000 0 -10000 0 0
RHOC 0.002 0.04 -10000 0 -0.35 4 4
RHOA -0.001 0.053 -10000 0 -0.34 9 9
cell motility 0.011 0.06 0.28 1 -0.35 5 6
PRL-1/alpha Tubulin -0.001 0.069 -10000 0 -10000 0 0
PRL-3/alpha1 Integrin 0.029 0.017 -10000 0 -0.24 1 1
ROCK1 0.011 0.06 0.28 1 -0.35 5 6
RABGGTB 0.023 0.002 -10000 0 -10000 0 0
CDK2 0.023 0.004 -10000 0 -10000 0 0
mitosis -0.027 0.055 -10000 0 -10000 0 0
ATF5 0.024 0.023 0.28 4 -10000 0 4
Caspase cascade in apoptosis

Figure S101.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S101.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TOP1 0.009 0.092 0.22 1 -0.41 16 17
ACTA1 0.011 0.067 0.21 7 -0.26 10 17
NUMA1 0.008 0.095 0.22 1 -0.38 20 21
SPTAN1 0.001 0.063 0.23 2 -0.27 10 12
LIMK1 0.003 0.07 0.24 11 -0.26 12 23
BIRC3 0.018 0.046 0.28 2 -0.35 7 9
BIRC2 0.022 0.004 -10000 0 -10000 0 0
BAX 0.023 0.004 -10000 0 -10000 0 0
CASP10 -0.009 0.038 0.26 2 -0.27 6 8
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0.023 0.002 -10000 0 -10000 0 0
PTK2 0.008 0.092 0.22 1 -0.39 17 18
DIABLO 0.023 0.003 -10000 0 -10000 0 0
apoptotic nuclear changes 0.001 0.062 0.22 2 -0.27 10 12
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.023 0.002 -10000 0 -10000 0 0
GSN -0.001 0.062 0.26 1 -0.28 10 11
MADD 0.022 0.005 -10000 0 -10000 0 0
TFAP2A 0.15 0.12 0.32 52 -0.62 6 58
BID 0.004 0.022 0.16 2 -0.17 5 7
MAP3K1 -0.008 0.1 -10000 0 -0.42 26 26
TRADD 0.02 0.008 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.033 0.007 -10000 0 -10000 0 0
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB 0.002 0.067 0.25 6 -0.26 12 18
CASP9 0.022 0.005 -10000 0 -10000 0 0
DNA repair -0.015 0.045 0.26 4 -0.19 1 5
neuron apoptosis 0.008 0.11 -10000 0 -0.83 8 8
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis 0.004 0.088 0.23 1 -0.36 18 19
APAF1 0.023 0.002 -10000 0 -10000 0 0
CASP6 -0.005 0.17 -10000 0 -0.88 17 17
TRAF2 0.022 0.006 -10000 0 -10000 0 0
ICAD/CAD 0 0.065 0.26 6 -0.33 5 11
CASP7 -0.002 0.059 0.25 6 -0.24 13 19
KRT18 0.017 0.057 -10000 0 -0.64 2 2
apoptosis 0.002 0.11 0.41 12 -0.42 18 30
DFFA 0.002 0.065 0.28 4 -0.27 10 14
DFFB 0.001 0.064 0.2 4 -0.27 11 15
PARP1 0.015 0.045 0.19 1 -0.27 4 5
actin filament polymerization -0.001 0.072 0.26 7 -0.29 12 19
TNF 0.053 0.089 0.28 64 -0.35 2 66
CYCS 0.007 0.042 0.17 8 -0.2 8 16
SATB1 -0.029 0.17 0.33 1 -0.83 18 19
SLK 0.004 0.073 0.32 9 -0.26 12 21
p15 BID/BAX 0.015 0.043 -10000 0 -0.17 8 8
CASP2 0.012 0.055 0.21 9 -0.29 6 15
JNK cascade 0.008 0.1 0.42 26 -10000 0 26
CASP3 0.004 0.067 0.21 4 -0.28 12 16
LMNB2 -0.014 0.16 0.26 3 -0.48 43 46
RIPK1 0.022 0.004 -10000 0 -10000 0 0
CASP4 0.021 0.017 -10000 0 -0.35 1 1
Mammalian IAPs/DIABLO 0.053 0.033 -10000 0 -0.19 7 7
negative regulation of DNA binding 0.15 0.12 0.32 52 -0.61 6 58
stress fiber formation 0.004 0.073 0.32 9 -0.26 12 21
GZMB -0.001 0.048 0.12 49 -0.28 5 54
CASP1 0.009 0.02 -10000 0 -0.26 3 3
LMNB1 0.006 0.12 0.23 7 -0.5 20 27
APP 0.007 0.12 -10000 0 -0.85 8 8
TNFRSF1A 0.022 0.004 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
CASP8 -0.006 0.001 -10000 0 -10000 0 0
VIM 0.002 0.1 0.32 10 -0.43 18 28
LMNA 0.01 0.087 0.25 3 -0.36 18 21
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD 0.014 0.058 0.22 3 -0.27 9 12
LRDD 0 0 -10000 0 -10000 0 0
SREBF1 0.004 0.065 0.2 9 -0.28 9 18
APAF-1/Caspase 9 0.006 0.098 -10000 0 -0.64 11 11
nuclear fragmentation during apoptosis 0.008 0.094 0.22 1 -0.38 20 21
CFL2 0.001 0.073 0.29 12 -0.26 8 20
GAS2 -0.011 0.075 0.21 2 -0.28 15 17
positive regulation of apoptosis 0 0.13 0.23 7 -0.49 25 32
PRF1 0.022 0.036 0.28 4 -0.35 3 7
ceramide signaling pathway

Figure S102.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S102.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K4 0.007 0.085 0.27 2 -0.39 12 14
BAG4 0.019 0.024 -10000 0 -0.35 2 2
BAD 0.005 0.043 0.18 10 -0.16 7 17
NFKBIA 0.022 0.004 -10000 0 -10000 0 0
BIRC3 0.018 0.046 0.28 2 -0.35 7 9
BAX 0.003 0.041 0.18 6 -0.16 8 14
EnzymeConsortium:3.1.4.12 0.003 0.025 0.075 8 -0.085 15 23
IKBKB 0.018 0.098 0.28 19 -0.38 9 28
MAP2K2 0.002 0.043 0.23 7 -0.16 3 10
MAP2K1 0.001 0.043 0.22 8 -0.17 4 12
SMPD1 0.001 0.033 -10000 0 -0.14 14 14
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 0.015 0.088 0.25 7 -0.36 14 21
MAP2K4 0.003 0.033 0.16 5 -0.16 3 8
protein ubiquitination 0.012 0.091 0.28 7 -0.37 11 18
EnzymeConsortium:2.7.1.37 0 0.048 0.21 10 -0.18 3 13
response to UV 0 0.001 0.003 8 -0.002 1 9
RAF1 0.003 0.045 0.22 8 -0.16 7 15
CRADD 0.023 0.002 -10000 0 -10000 0 0
mol:ceramide 0.005 0.039 0.11 9 -0.14 14 23
I-kappa-B-alpha/RELA/p50/ubiquitin 0.029 0.008 -10000 0 -10000 0 0
MADD 0.022 0.005 -10000 0 -10000 0 0
MAP3K1 0.004 0.037 0.15 7 -0.15 9 16
TRADD 0.02 0.008 -10000 0 -10000 0 0
RELA/p50 0.022 0.004 -10000 0 -10000 0 0
MAPK3 0.002 0.049 0.21 9 -0.18 5 14
MAPK1 0 0.053 0.21 9 -0.22 7 16
p50/RELA/I-kappa-B-alpha 0.032 0.008 -10000 0 -10000 0 0
FADD 0.009 0.083 0.22 6 -0.38 12 18
KSR1 0.004 0.041 0.17 7 -0.16 9 16
MAPK8 0.001 0.041 0.16 9 -0.15 5 14
TRAF2 0.021 0.006 -10000 0 -10000 0 0
response to radiation 0 0 0.002 4 -10000 0 4
CHUK 0.007 0.085 0.26 6 -0.38 11 17
TNF R/SODD 0.029 0.021 -10000 0 -0.24 2 2
TNF 0.053 0.089 0.28 64 -0.35 2 66
CYCS 0.013 0.049 0.16 18 -0.16 6 24
IKBKG 0.006 0.087 0.29 6 -0.39 10 16
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD 0.011 0.086 0.21 3 -0.42 11 14
RELA 0.022 0.004 -10000 0 -10000 0 0
RIPK1 0.022 0.004 -10000 0 -10000 0 0
AIFM1 0.012 0.047 0.15 16 -0.16 5 21
TNF/TNF R/SODD 0.054 0.054 0.2 50 -0.21 2 52
TNFRSF1A 0.022 0.004 -10000 0 -10000 0 0
response to heat 0 0 0.002 4 -10000 0 4
CASP8 0.017 0.081 -10000 0 -0.67 6 6
NSMAF 0.017 0.089 0.24 12 -0.41 9 21
response to hydrogen peroxide 0 0.001 0.003 8 -0.002 1 9
BCL2 -0.01 0.1 -10000 0 -0.35 44 44
Role of Calcineurin-dependent NFAT signaling in lymphocytes

Figure S103.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S103.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.022 0.015 0.33 1 -10000 0 1
NFATC1 0.012 0.078 0.28 4 -0.44 3 7
NFATC2 -0.001 0.066 0.14 9 -0.21 21 30
NFATC3 0.012 0.016 -10000 0 -0.3 1 1
YWHAE 0.021 0.007 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/CABIN1 -0.022 0.12 0.21 4 -0.36 33 37
Exportin 1/Ran/NUP214 0.042 0.014 -10000 0 -10000 0 0
mol:DAG 0 0.001 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV 0.002 0.1 -10000 0 -0.32 26 26
BCL2/BAX 0.008 0.078 -10000 0 -0.24 44 44
CaM/Ca2+/Calcineurin A alpha-beta B1 0.015 0.01 -10000 0 -10000 0 0
CaM/Ca2+ 0.015 0.01 -10000 0 -10000 0 0
BAX 0.023 0.004 -10000 0 -10000 0 0
MAPK14 0.022 0.006 -10000 0 -10000 0 0
BAD 0.022 0.004 -10000 0 -10000 0 0
CABIN1/MEF2D -0.009 0.1 0.19 1 -0.34 27 28
Calcineurin A alpha-beta B1/BCL2 -0.009 0.1 -10000 0 -0.35 44 44
FKBP8 0.022 0.005 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.009 0.1 0.34 27 -0.19 1 28
KPNB1 0.022 0.005 -10000 0 -10000 0 0
KPNA2 0.034 0.057 0.3 23 -10000 0 23
XPO1 0.023 0.003 -10000 0 -10000 0 0
SFN 0.21 0.12 0.28 372 -10000 0 372
MAP3K8 0.02 0.029 -10000 0 -0.35 3 3
NFAT4/CK1 alpha 0.017 0.022 -10000 0 -0.16 1 1
MEF2D/NFAT1/Cbp/p300 0.013 0.087 -10000 0 -0.24 32 32
CABIN1 -0.022 0.12 0.21 4 -0.36 32 36
CALM1 0.02 0.01 -10000 0 -10000 0 0
RAN 0.023 0.003 -10000 0 -10000 0 0
MAP3K1 0.022 0.005 -10000 0 -10000 0 0
CAMK4 0.022 0.038 0.28 5 -0.35 3 8
mol:Ca2+ 0 0.003 -10000 0 -10000 0 0
MAPK3 0.022 0.005 -10000 0 -10000 0 0
YWHAH 0.022 0.006 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/AKAP79/PKA 0.03 0.02 -10000 0 -0.24 2 2
YWHAB 0.022 0.005 -10000 0 -10000 0 0
MAPK8 0.018 0.037 -10000 0 -0.35 5 5
MAPK9 0.022 0.004 -10000 0 -10000 0 0
YWHAG 0.022 0.004 -10000 0 -10000 0 0
FKBP1A 0.022 0.004 -10000 0 -10000 0 0
NFAT1-c-4/YWHAQ 0.013 0.085 0.26 3 -0.38 6 9
PRKCH 0.021 0.023 -10000 0 -0.35 2 2
CABIN1/Cbp/p300 0.028 0.018 -10000 0 -10000 0 0
CASP3 0.021 0.006 -10000 0 -10000 0 0
PIM1 0.023 0.003 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.014 0.007 -10000 0 -10000 0 0
apoptosis 0.007 0.031 0.19 1 -0.25 2 3
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0.049 0.058 0.2 6 -0.29 6 12
PRKCB 0 0.088 -10000 0 -0.35 31 31
PRKCE 0.023 0.003 -10000 0 -10000 0 0
JNK2/NFAT4 0.012 0.053 -10000 0 -0.27 1 1
BAD/BCL-XL 0.032 0.013 0.24 1 -10000 0 1
PRKCD 0.022 0.005 -10000 0 -10000 0 0
NUP214 0.021 0.006 -10000 0 -10000 0 0
PRKCZ 0.022 0.021 0.28 1 -0.35 1 2
PRKCA 0 0.087 -10000 0 -0.35 30 30
PRKCG 0.049 0.096 0.28 64 -0.35 6 70
PRKCQ -0.007 0.1 0.28 1 -0.35 42 43
FKBP38/BCL2 0.008 0.078 -10000 0 -0.24 44 44
EP300 0.019 0.012 -10000 0 -10000 0 0
PRKCB1 0 0 -10000 0 -10000 0 0
CSNK2A1 0.022 0.004 -10000 0 -10000 0 0
NFATc/JNK1 0.023 0.078 0.28 3 -0.42 3 6
CaM/Ca2+/FKBP38 0.026 0.015 -10000 0 -10000 0 0
FKBP12/FK506 0.017 0.003 -10000 0 -10000 0 0
CSNK1A1 0.008 0.009 -10000 0 -10000 0 0
CaM/Ca2+/CAMK IV 0.027 0.027 0.19 5 -0.2 3 8
NFATc/ERK1 0.023 0.077 0.28 3 -0.41 3 6
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV 0.002 0.11 -10000 0 -0.32 32 32
NR4A1 0.011 0.12 0.23 14 -0.38 29 43
GSK3B 0.022 0.006 -10000 0 -10000 0 0
positive T cell selection 0.012 0.016 -10000 0 -0.3 1 1
NFAT1/CK1 alpha 0.002 0.048 0.12 1 -0.2 9 10
RCH1/ KPNB1 0.04 0.039 0.22 22 -10000 0 22
YWHAQ 0.022 0.005 -10000 0 -10000 0 0
PRKACA 0.021 0.006 -10000 0 -10000 0 0
AKAP5 0.021 0.023 -10000 0 -0.35 2 2
MEF2D 0.016 0.013 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.021 0.007 -10000 0 -10000 0 0
NFATc/p38 alpha 0.022 0.076 0.28 3 -0.42 3 6
CREBBP 0.019 0.012 -10000 0 -10000 0 0
BCL2 -0.01 0.1 -10000 0 -0.35 44 44
ErbB4 signaling events

Figure S104.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S104.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ErbB4/ErbB4/HBEGF/HBEGF 0.027 0.053 -10000 0 -10000 0 0
epithelial cell differentiation -0.009 0.089 -10000 0 -0.35 3 3
ITCH 0.016 0.024 -10000 0 -10000 0 0
WWP1 0.019 0.054 -10000 0 -10000 0 0
FYN 0.022 0.004 -10000 0 -10000 0 0
EGFR 0.014 0.06 0.33 1 -0.35 13 14
PRL 0.012 0.066 0.28 4 -0.35 15 19
neuron projection morphogenesis 0.036 0.095 0.28 27 -10000 0 27
PTPRZ1 0.033 0.059 0.28 28 -10000 0 28
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC 0.028 0.05 -10000 0 -10000 0 0
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta 0.009 0.041 -10000 0 -0.26 2 2
ADAM17 0.016 0.024 -10000 0 -10000 0 0
ErbB4/ErbB4 0.017 0.048 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 3/neuregulin 3 0.03 0.065 0.26 2 -10000 0 2
NCOR1 0.021 0.007 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn 0.018 0.045 -10000 0 -0.25 2 2
GRIN2B 0.016 0.062 0.25 13 -0.24 2 15
ErbB4/ErbB2/betacellulin 0.022 0.06 0.25 7 -10000 0 7
STAT1 0.023 0.012 0.28 1 -10000 0 1
HBEGF 0.023 0.004 -10000 0 -10000 0 0
PRLR -0.049 0.15 -10000 0 -0.35 99 99
E4ICDs/ETO2 0.006 0.075 -10000 0 -0.3 3 3
axon guidance 0.013 0.048 -10000 0 -10000 0 0
NEDD4 -0.012 0.092 -10000 0 -0.35 34 34
Prolactin receptor/Prolactin receptor/Prolactin -0.026 0.12 0.21 3 -0.26 106 109
CBFA2T3 -0.024 0.12 -10000 0 -0.35 62 62
ErbB4/ErbB2/HBEGF 0.029 0.049 0.28 3 -10000 0 3
MAPK3 0.03 0.083 0.27 15 -10000 0 15
STAT1 (dimer) 0.026 0.053 -10000 0 -10000 0 0
MAPK1 0.03 0.084 0.27 15 -10000 0 15
JAK2 0.016 0.049 -10000 0 -0.35 9 9
ErbB4/ErbB2/neuregulin 1 beta 0.012 0.051 0.25 7 -0.25 2 9
NRG1 -0.012 0.033 -10000 0 -0.25 8 8
NRG3 0.03 0.052 0.29 20 -10000 0 20
NRG2 -0.027 0.12 -10000 0 -0.35 68 68
NRG4 0.044 0.073 0.28 45 -10000 0 45
heart development 0.013 0.048 -10000 0 -10000 0 0
neural crest cell migration 0.012 0.051 0.25 7 -0.25 2 9
ERBB2 0.001 0.052 0.3 14 -10000 0 14
WWOX/E4ICDs 0.025 0.049 -10000 0 -10000 0 0
SHC1 0.019 0.009 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 4 0.043 0.077 0.3 2 -0.28 2 4
apoptosis -0.032 0.06 0.31 2 -0.27 2 4
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta 0.005 0.081 -10000 0 -0.3 6 6
ErbB4/ErbB2/epiregulin 0.05 0.082 0.31 16 -10000 0 16
ErbB4/ErbB4/betacellulin/betacellulin 0.02 0.065 -10000 0 -0.26 2 2
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 0.006 0.11 -10000 0 -0.3 20 20
MDM2 0.013 0.047 0.26 3 -10000 0 3
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta 0.016 0.036 -10000 0 -0.23 2 2
STAT5A 0.01 0.051 0.28 1 -10000 0 1
ErbB4/EGFR/neuregulin 1 beta 0.015 0.056 0.27 1 -0.31 5 6
DLG4 0.02 0.024 -10000 0 -0.35 2 2
GRB2/SHC 0.026 0.015 -10000 0 -10000 0 0
E4ICDs/TAB2/NCoR1 0.022 0.047 -10000 0 -10000 0 0
STAT5A (dimer) -0.001 0.1 -10000 0 -0.38 3 3
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) 0.024 0.057 -10000 0 -10000 0 0
LRIG1 0.02 0.029 -10000 0 -0.35 3 3
EREG 0.055 0.087 0.28 67 -10000 0 67
BTC 0.01 0.066 -10000 0 -0.35 17 17
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta 0.009 0.04 -10000 0 -10000 0 0
ERBB4 0.017 0.048 -10000 0 -10000 0 0
STAT5B 0.02 0.024 -10000 0 -0.35 2 2
YAP1 0.013 0.074 -10000 0 -0.45 11 11
GRB2 0.022 0.006 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 0.043 0.072 0.34 11 -10000 0 11
glial cell differentiation -0.022 0.046 -10000 0 -10000 0 0
WWOX 0.02 0.008 -10000 0 -10000 0 0
cell proliferation 0.013 0.088 0.28 8 -0.36 3 11
E-cadherin signaling in keratinocytes

Figure S105.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S105.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
keratinocyte differentiation 0.004 0.061 0.2 2 -0.24 15 17
adherens junction organization -0.008 0.09 0.29 1 -0.36 22 23
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.012 0.062 0.21 2 -0.26 3 5
FMN1 -0.003 0.076 -10000 0 -0.31 21 21
mol:IP3 0 0.042 -10000 0 -0.22 6 6
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.003 0.086 -10000 0 -0.31 27 27
CTNNB1 0.023 0.006 -10000 0 -10000 0 0
AKT1 -0.001 0.051 -10000 0 -0.25 8 8
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.007 0.12 -10000 0 -0.54 15 15
CTNND1 0.024 0.006 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.008 0.073 -10000 0 -0.3 22 22
VASP -0.007 0.08 -10000 0 -0.29 26 26
ZYX -0.007 0.079 -10000 0 -0.3 25 25
JUB -0.005 0.081 -10000 0 -0.29 27 27
EGFR(dimer) 0.001 0.095 0.26 1 -0.3 31 32
E-cadherin/beta catenin-gamma catenin 0.038 0.026 -10000 0 -0.27 2 2
mol:PI-3-4-5-P3 0.014 0.061 -10000 0 -0.24 11 11
PIK3CA 0.02 0.018 -10000 0 -0.35 1 1
PI3K 0.014 0.062 -10000 0 -0.24 11 11
FYN 0.004 0.053 0.18 4 -0.29 4 8
mol:Ca2+ 0 0.041 -10000 0 -0.21 6 6
JUP 0.022 0.017 -10000 0 -0.34 1 1
PIK3R1 0.019 0.037 -10000 0 -0.35 5 5
mol:DAG 0 0.042 -10000 0 -0.22 6 6
CDH1 0.019 0.024 -10000 0 -0.35 2 2
RhoA/GDP 0.013 0.063 0.21 1 -0.32 3 4
establishment of polarity of embryonic epithelium -0.008 0.08 -10000 0 -0.29 27 27
SRC 0.022 0.005 -10000 0 -10000 0 0
RAC1 0.022 0.005 -10000 0 -10000 0 0
RHOA 0.022 0.005 -10000 0 -10000 0 0
EGFR 0.014 0.06 0.33 1 -0.35 13 14
CASR 0.001 0.054 0.16 19 -0.21 5 24
RhoA/GTP 0.017 0.052 -10000 0 -0.21 4 4
AKT2 -0.002 0.052 -10000 0 -0.24 10 10
actin cable formation -0.003 0.074 0.2 8 -0.31 17 25
apoptosis -0.008 0.073 0.24 17 -0.24 10 27
CTNNA1 0.023 0.006 -10000 0 -10000 0 0
mol:GDP -0.001 0.058 0.15 25 -0.25 7 32
PIP5K1A -0.008 0.072 -10000 0 -0.3 21 21
PLCG1 0 0.043 -10000 0 -0.22 6 6
Rac1/GTP 0.009 0.091 0.24 1 -0.29 27 28
homophilic cell adhesion 0 0.003 -10000 0 -10000 0 0
Paxillin-independent events mediated by a4b1 and a4b7

Figure S106.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S106.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0.014 0.015 -10000 0 -0.27 1 1
CRKL 0.022 0.005 -10000 0 -10000 0 0
Rac1/GDP 0.016 0.003 -10000 0 -10000 0 0
DOCK1 0.018 0.04 -10000 0 -0.35 6 6
ITGA4 0.022 0.026 0.28 1 -0.35 2 3
alpha4/beta7 Integrin/MAdCAM1 0.063 0.047 0.21 40 -0.19 1 41
EPO 0.011 0.063 0.28 1 -0.35 15 16
alpha4/beta7 Integrin 0.033 0.017 0.21 2 -0.24 1 3
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.021 0.006 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.032 0.02 0.21 1 -0.24 2 3
EPO/EPOR (dimer) 0.025 0.054 0.23 8 -0.24 15 23
lamellipodium assembly 0.013 0.075 -10000 0 -0.4 9 9
PIK3CA 0.02 0.018 -10000 0 -0.35 1 1
PI3K 0.026 0.03 -10000 0 -0.24 5 5
ARF6 0.023 0.003 -10000 0 -10000 0 0
JAK2 0.009 0.049 0.17 4 -0.21 21 25
PXN 0.023 0.003 -10000 0 -10000 0 0
PIK3R1 0.018 0.037 -10000 0 -0.35 5 5
MADCAM1 0.04 0.07 0.28 40 -10000 0 40
cell adhesion 0.061 0.046 0.2 40 -0.19 1 41
CRKL/CBL 0.031 0.01 -10000 0 -10000 0 0
ITGB1 0.022 0.004 -10000 0 -10000 0 0
SRC -0.021 0.058 0.18 15 -0.2 33 48
ITGB7 0.023 0.012 0.28 1 -10000 0 1
RAC1 0.022 0.005 -10000 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 0.027 0.069 0.2 1 -0.22 36 37
p130Cas/Crk/Dock1 0.008 0.056 0.18 5 -0.38 2 7
VCAM1 -0.005 0.098 -10000 0 -0.35 39 39
RHOA 0.022 0.005 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.053 0.024 -10000 0 -0.19 2 2
BCAR1 -0.019 0.051 0.18 13 -0.19 26 39
EPOR 0.026 0.034 0.31 7 -10000 0 7
mol:GDP 0 0 -10000 0 -10000 0 0
CBL 0.022 0.005 -10000 0 -10000 0 0
GIT1 0.022 0.005 -10000 0 -10000 0 0
Rac1/GTP 0.013 0.077 -10000 0 -0.42 9 9
Signaling mediated by p38-gamma and p38-delta

Figure S107.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S107.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EEF2K -0.011 0.017 0.24 2 -10000 0 2
SNTA1 0.022 0.005 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
STMN1 -0.011 0.017 0.24 2 -10000 0 2
MAPK12 -0.007 0.045 0.2 5 -0.2 20 25
CCND1 0.004 0.034 -10000 0 -0.33 3 3
p38 gamma/SNTA1 0.014 0.057 0.23 12 -0.19 20 32
MAP2K3 0.021 0.006 -10000 0 -10000 0 0
PKN1 0.022 0.006 -10000 0 -10000 0 0
G2/M transition checkpoint -0.005 0.049 0.22 9 -0.2 20 29
MAP2K6 -0.002 0.046 0.2 2 -0.22 20 22
MAPT -0.004 0.064 0.23 6 -0.25 21 27
MAPK13 -0.008 0.022 0.17 6 -10000 0 6
hyperosmotic response 0 0 -10000 0 -10000 0 0
ZAK -0.001 0.053 -10000 0 -0.26 22 22
Stabilization and expansion of the E-cadherin adherens junction

Figure S108.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S108.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
adherens junction organization 0.013 0.024 -10000 0 -0.17 8 8
epithelial cell differentiation 0.041 0.023 -10000 0 -0.18 2 2
CYFIP2 0.02 0.028 -10000 0 -0.35 3 3
ENAH -0.006 0.057 0.26 13 -10000 0 13
EGFR 0.014 0.06 0.33 1 -0.35 13 14
EPHA2 0.022 0.005 -10000 0 -10000 0 0
MYO6 -0.012 0.025 0.17 6 -10000 0 6
CTNNB1 0.022 0.004 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 0.043 0.017 -10000 0 -0.21 1 1
AQP5 0.077 0.086 0.23 7 -0.34 8 15
CTNND1 0.023 0.003 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.014 0.017 0.17 2 -10000 0 2
regulation of calcium-dependent cell-cell adhesion -0.016 0.036 0.17 6 -0.32 1 7
EGF 0.031 0.052 0.28 20 -0.35 1 21
NCKAP1 0.023 0.003 -10000 0 -10000 0 0
AQP3 -0.001 0.058 -10000 0 -0.3 15 15
cortical microtubule organization 0.041 0.023 -10000 0 -0.18 2 2
GO:0000145 -0.013 0.016 0.16 2 -10000 0 2
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.046 0.024 -10000 0 -0.18 2 2
MLLT4 0.022 0.005 -10000 0 -10000 0 0
ARF6/GDP -0.02 0.018 -10000 0 -0.16 4 4
ARF6 0.023 0.003 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.043 0.031 -10000 0 -0.19 2 2
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP -0.004 0.017 -10000 0 -10000 0 0
PVRL2 0.022 0.005 -10000 0 -10000 0 0
ZYX -0.012 0.023 0.17 5 -10000 0 5
ARF6/GTP 0.047 0.033 -10000 0 -0.18 2 2
CDH1 0.019 0.024 -10000 0 -0.35 2 2
EGFR/EGFR/EGF/EGF 0.033 0.043 -10000 0 -0.18 13 13
RhoA/GDP 0.042 0.023 -10000 0 -0.17 2 2
actin cytoskeleton organization -0.014 0.021 0.16 5 -10000 0 5
IGF-1R heterotetramer 0.008 0.07 -10000 0 -0.35 19 19
GIT1 0.022 0.005 -10000 0 -10000 0 0
IGF1R 0.008 0.07 -10000 0 -0.35 19 19
IGF1 -0.048 0.15 -10000 0 -0.35 99 99
DIAPH1 0.019 0.096 -10000 0 -0.53 7 7
Wnt receptor signaling pathway -0.041 0.023 0.18 2 -10000 0 2
RHOA 0.022 0.005 -10000 0 -10000 0 0
RhoA/GTP -0.02 0.018 -10000 0 -0.16 4 4
CTNNA1 0.023 0.004 -10000 0 -10000 0 0
VCL -0.015 0.021 0.16 5 -10000 0 5
EFNA1 0.02 0.02 0.3 2 -10000 0 2
LPP -0.014 0.023 0.17 5 -10000 0 5
Ephrin A1/EPHA2 0.029 0.026 -10000 0 -0.17 2 2
SEC6/SEC8 -0.021 0.012 -10000 0 -0.17 1 1
MGAT3 -0.016 0.037 0.17 6 -0.32 1 7
HGF/MET -0.002 0.087 -10000 0 -0.18 95 95
HGF -0.048 0.14 -10000 0 -0.35 98 98
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN 0.013 0.024 -10000 0 -0.17 8 8
actin cable formation 0.047 0.11 0.23 93 -0.24 2 95
KIAA1543 -0.013 0.022 0.16 5 -0.16 3 8
KIFC3 -0.014 0.022 0.17 5 -10000 0 5
NCK1 0.021 0.023 -10000 0 -0.35 2 2
EXOC3 0.022 0.006 -10000 0 -10000 0 0
ACTN1 -0.012 0.024 0.17 6 -10000 0 6
NCK1/GIT1 0.03 0.02 -10000 0 -0.24 2 2
mol:GDP 0.041 0.023 -10000 0 -0.18 2 2
EXOC4 0.022 0.005 -10000 0 -10000 0 0
STX4 -0.012 0.024 0.17 6 -0.17 2 8
PIP5K1C -0.014 0.017 0.17 2 -10000 0 2
LIMA1 0.023 0.003 -10000 0 -10000 0 0
ABI1 0.022 0.005 -10000 0 -10000 0 0
ROCK1 0.018 0.087 0.31 17 -10000 0 17
adherens junction assembly -0.043 0.14 -10000 0 -0.56 29 29
IGF-1R heterotetramer/IGF1 -0.008 0.093 -10000 0 -0.18 106 106
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.031 0.01 -10000 0 -10000 0 0
MET 0.021 0.04 0.28 4 -0.35 4 8
PLEKHA7 -0.013 0.024 0.17 5 -0.17 1 6
mol:GTP 0.041 0.03 -10000 0 -0.19 2 2
establishment of epithelial cell apical/basal polarity 0 0.075 0.34 12 -10000 0 12
cortical actin cytoskeleton stabilization 0.013 0.024 -10000 0 -0.17 8 8
regulation of cell-cell adhesion -0.014 0.021 0.16 5 -10000 0 5
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton 0.013 0.024 -10000 0 -0.17 8 8
IL27-mediated signaling events

Figure S109.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S109.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.023 0.017 -10000 0 -0.35 1 1
CD4-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
cytokine production during immune response 0.013 0.11 0.42 10 -0.37 1 11
IL27/IL27R/JAK1 0.026 0.12 0.47 4 -0.95 2 6
TBX21 -0.017 0.11 0.36 3 -0.4 9 12
IL12B 0.022 0.013 0.28 1 -10000 0 1
IL12A -0.003 0.032 0.14 11 -0.24 4 15
IL6ST -0.032 0.13 -10000 0 -0.35 74 74
IL27RA/JAK1 0.017 0.084 -10000 0 -1 2 2
IL27 0.025 0.043 0.29 12 -10000 0 12
TYK2 0.022 0.014 -10000 0 -10000 0 0
T-helper cell lineage commitment 0.006 0.066 0.44 2 -0.38 1 3
T-helper 2 cell differentiation 0.013 0.11 0.42 10 -0.37 1 11
T cell proliferation during immune response 0.013 0.11 0.42 10 -0.37 1 11
MAPKKK cascade -0.013 0.11 0.37 1 -0.42 10 11
STAT3 0.022 0.006 -10000 0 -10000 0 0
STAT2 0.023 0.003 -10000 0 -10000 0 0
STAT1 0.023 0.012 0.29 1 -10000 0 1
IL12RB1 0.026 0.053 0.29 13 -0.35 4 17
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.008 0.11 0.36 7 -0.51 3 10
IL27/IL27R/JAK2/TYK2 -0.011 0.11 0.37 1 -0.44 8 9
positive regulation of T cell mediated cytotoxicity -0.013 0.11 0.37 1 -0.42 10 11
STAT1 (dimer) 0.018 0.14 0.59 5 -0.72 3 8
JAK2 0.017 0.05 -10000 0 -0.35 9 9
JAK1 0.022 0.017 -10000 0 -0.35 1 1
STAT2 (dimer) -0.005 0.12 0.34 1 -0.41 10 11
T cell proliferation -0.019 0.11 0.35 1 -0.42 12 13
IL12/IL12R/TYK2/JAK2 0.004 0.17 -10000 0 -0.71 26 26
IL17A 0.006 0.064 0.44 2 -0.38 1 3
mast cell activation 0.013 0.11 0.42 10 -0.37 1 11
IFNG 0.007 0.034 0.1 12 -0.091 12 24
T cell differentiation -0.001 0.005 0.013 3 -0.018 12 15
STAT3 (dimer) -0.004 0.12 0.34 1 -0.41 11 12
STAT5A (dimer) -0.004 0.12 0.34 1 -0.41 11 12
STAT4 (dimer) -0.006 0.12 0.34 1 -0.42 11 12
STAT4 0.022 0.017 -10000 0 -0.35 1 1
T cell activation -0.005 0.01 0.12 2 -0.087 2 4
IL27R/JAK2/TYK2 0.008 0.11 -10000 0 -0.98 2 2
GATA3 0.003 0.16 0.61 15 -1.1 6 21
IL18 -0.003 0.014 0.11 8 -10000 0 8
positive regulation of mast cell cytokine production -0.004 0.12 0.33 1 -0.4 11 12
IL27/EBI3 0.039 0.049 0.25 20 -10000 0 20
IL27RA 0.004 0.085 0.37 1 -1.1 2 3
IL6 0.017 0.07 0.28 9 -0.35 14 23
STAT5A 0.021 0.017 -10000 0 -0.35 1 1
monocyte differentiation 0 0.001 -10000 0 -10000 0 0
IL2 -0.007 0.038 0.43 2 -10000 0 2
IL1B -0.006 0.021 -10000 0 -0.24 4 4
EBI3 0.027 0.044 0.29 13 -10000 0 13
TNF 0.009 0.043 0.11 64 -0.24 2 66
E-cadherin signaling in the nascent adherens junction

Figure S110.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S110.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN -0.016 0.091 -10000 0 -0.27 57 57
KLHL20 -0.005 0.062 0.2 2 -0.2 28 30
CYFIP2 0.02 0.028 -10000 0 -0.35 3 3
Rac1/GDP 0.001 0.068 0.25 3 -0.26 7 10
ENAH -0.019 0.093 -10000 0 -0.28 58 58
AP1M1 0.022 0.005 -10000 0 -10000 0 0
RAP1B 0.023 0.002 -10000 0 -10000 0 0
RAP1A 0.023 0.001 -10000 0 -10000 0 0
CTNNB1 0.022 0.004 -10000 0 -10000 0 0
CDC42/GTP 0.014 0.027 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 -0.013 0.037 -10000 0 -0.14 29 29
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin 0.048 0.028 0.21 1 -0.19 2 3
RAPGEF1 -0.012 0.079 0.22 2 -0.31 9 11
CTNND1 0.023 0.003 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.012 0.1 -10000 0 -0.28 63 63
CRK -0.009 0.082 -10000 0 -0.27 42 42
E-cadherin/gamma catenin/alpha catenin 0.039 0.027 -10000 0 -0.3 2 2
alphaE/beta7 Integrin 0.032 0.013 0.21 1 -10000 0 1
IQGAP1 0.022 0.004 -10000 0 -10000 0 0
NCKAP1 0.023 0.003 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.042 0.01 -10000 0 -10000 0 0
DLG1 -0.013 0.087 -10000 0 -0.27 50 50
ChemicalAbstracts:7440-70-2 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.016 0.016 -10000 0 -0.13 2 2
MLLT4 0.022 0.005 -10000 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 0.036 0.036 -10000 0 -0.18 12 12
PI3K -0.02 0.02 -10000 0 -10000 0 0
ARF6 0.023 0.003 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
E-cadherin/gamma catenin 0.028 0.027 -10000 0 -0.34 2 2
TIAM1 0.013 0.058 -10000 0 -0.35 13 13
E-cadherin(dimer)/Ca2+ 0.046 0.025 -10000 0 -0.18 2 2
AKT1 -0.012 0.02 -10000 0 -10000 0 0
PIK3R1 0.018 0.037 -10000 0 -0.35 5 5
CDH1 0.019 0.024 -10000 0 -0.35 2 2
RhoA/GDP 0 0.067 0.23 1 -0.26 5 6
actin cytoskeleton organization -0.003 0.048 0.17 3 -0.15 28 31
CDC42/GDP 0.002 0.068 0.25 3 -0.27 6 9
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin 0.012 0.02 -10000 0 -0.28 2 2
ITGB7 0.023 0.012 0.28 1 -10000 0 1
RAC1 0.022 0.005 -10000 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin 0.049 0.026 -10000 0 -0.19 2 2
E-cadherin/Ca2+/beta catenin/alpha catenin 0.034 0.02 -10000 0 -0.17 2 2
mol:GDP -0.011 0.073 0.25 3 -0.29 9 12
CDC42/GTP/IQGAP1 0.029 0.008 -10000 0 -10000 0 0
JUP 0.021 0.017 -10000 0 -0.35 1 1
p120 catenin/RhoA/GDP 0.008 0.069 0.24 1 -0.27 4 5
RAC1/GTP/IQGAP1 0.029 0.008 -10000 0 -10000 0 0
PIP5K1C/AP1M1 0.031 0.011 -10000 0 -10000 0 0
RHOA 0.022 0.005 -10000 0 -10000 0 0
CDC42 0.022 0.004 -10000 0 -10000 0 0
CTNNA1 0.023 0.004 -10000 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle 0.004 0.036 0.16 5 -0.1 12 17
NME1 0.022 0.005 -10000 0 -10000 0 0
clathrin coat assembly 0 0 -10000 0 -10000 0 0
TJP1 -0.01 0.084 -10000 0 -0.27 48 48
regulation of cell-cell adhesion 0.008 0.023 -10000 0 -10000 0 0
WASF2 -0.001 0.025 -10000 0 -10000 0 0
Rap1/GTP 0.017 0.037 -10000 0 -10000 0 0
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin 0.056 0.034 -10000 0 -0.26 2 2
CCND1 0.004 0.043 0.19 5 -0.12 12 17
VAV2 -0.03 0.16 -10000 0 -0.56 34 34
RAP1/GDP 0.017 0.06 0.25 4 -0.26 3 7
adherens junction assembly -0.011 0.084 -10000 0 -0.26 50 50
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
ABI1 0.022 0.005 -10000 0 -10000 0 0
PIP5K1C 0.021 0.006 -10000 0 -10000 0 0
regulation of heterotypic cell-cell adhesion 0.04 0.029 -10000 0 -0.25 2 2
E-cadherin/beta catenin 0.008 0.019 -10000 0 -0.29 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
SRC -0.016 0.092 -10000 0 -0.27 57 57
PIK3CA 0.02 0.018 -10000 0 -0.35 1 1
Rac1/GTP -0.018 0.085 -10000 0 -0.31 29 29
E-cadherin/beta catenin/alpha catenin 0.039 0.023 -10000 0 -0.21 2 2
ITGAE 0.021 0.006 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.013 0.1 -10000 0 -0.28 63 63
Class IB PI3K non-lipid kinase events

Figure S111.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S111.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
cAMP biosynthetic process -0.022 0.043 0.35 4 -0.29 6 10
PI3K Class IB/PDE3B 0.022 0.044 0.29 6 -0.35 4 10
PDE3B 0.022 0.044 0.29 6 -0.35 4 10
Canonical NF-kappaB pathway

Figure S112.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S112.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
FBXW11 0.024 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.016 0.093 0.26 6 -0.3 19 25
ERC1 0.022 0.004 -10000 0 -10000 0 0
RIP2/NOD2 0.029 0.015 0.21 1 -10000 0 1
NFKBIA -0.008 0.027 0.2 7 -10000 0 7
BIRC2 0.022 0.004 -10000 0 -10000 0 0
IKBKB 0.021 0.007 -10000 0 -10000 0 0
RIPK2 0.021 0.007 -10000 0 -10000 0 0
IKBKG 0.016 0.018 -10000 0 -10000 0 0
IKK complex/A20 0.033 0.11 -10000 0 -0.34 32 32
NEMO/A20/RIP2 0.021 0.007 -10000 0 -10000 0 0
XPO1 0.023 0.003 -10000 0 -10000 0 0
NEMO/ATM 0.01 0.11 0.26 1 -0.35 37 38
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
RAN 0.023 0.003 -10000 0 -10000 0 0
Exportin 1/RanGTP 0.03 0.006 -10000 0 -10000 0 0
IKK complex/ELKS 0.013 0.098 -10000 0 -0.32 34 34
BCL10/MALT1/TRAF6 0.043 0.013 -10000 0 -10000 0 0
NOD2 0.022 0.013 0.28 1 -10000 0 1
NFKB1 0.023 0.017 -10000 0 -0.35 1 1
RELA 0.023 0.004 -10000 0 -10000 0 0
MALT1 0.022 0.005 -10000 0 -10000 0 0
cIAP1/UbcH5C 0.032 0.009 -10000 0 -10000 0 0
ATM 0.022 0.005 -10000 0 -10000 0 0
TNF/TNFR1A 0.052 0.061 0.21 61 -0.24 2 63
TRAF6 0.022 0.005 -10000 0 -10000 0 0
PRKCA 0 0.087 -10000 0 -0.35 30 30
CHUK 0.022 0.005 -10000 0 -10000 0 0
UBE2D3 0.022 0.004 -10000 0 -10000 0 0
TNF 0.053 0.089 0.28 64 -0.35 2 66
NF kappa B1 p50/RelA 0.047 0.018 -10000 0 -0.2 1 1
BCL10 0.023 0.002 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.008 0.026 0.2 7 -10000 0 7
beta TrCP1/SCF ubiquitin ligase complex 0.024 0.004 -10000 0 -10000 0 0
TNFRSF1A 0.022 0.004 -10000 0 -10000 0 0
IKK complex 0.014 0.1 0.26 1 -0.34 34 35
CYLD 0.021 0.006 -10000 0 -10000 0 0
IKK complex/PKC alpha 0.012 0.11 -10000 0 -0.35 33 33
Signaling events mediated by HDAC Class III

Figure S113.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S113.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EP300 0.021 0.006 -10000 0 -10000 0 0
HDAC4 0.023 0.004 -10000 0 -10000 0 0
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle 0.008 0.034 0.25 2 -0.23 7 9
CDKN1A -0.008 0.007 -10000 0 -10000 0 0
KAT2B 0.017 0.046 -10000 0 -0.35 8 8
BAX 0.023 0.004 -10000 0 -10000 0 0
FOXO3 -0.003 0.006 -10000 0 -10000 0 0
FOXO1 0.02 0.024 -10000 0 -0.35 2 2
FOXO4 0.009 0.015 -10000 0 -0.22 2 2
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.022 0.006 -10000 0 -10000 0 0
TAT 0.019 0.014 0.28 1 -10000 0 1
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 -0.006 0.05 0.12 43 -0.24 8 51
PPARGC1A -0.052 0.15 0.28 2 -0.35 105 107
FHL2 0.019 0.036 -10000 0 -0.35 5 5
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.029 0.02 -10000 0 -0.25 2 2
HIST2H4A -0.008 0.034 0.23 7 -0.25 2 9
SIRT1/FOXO3a 0.016 0.033 -10000 0 -0.2 7 7
SIRT1 0.019 0.023 -10000 0 -0.35 2 2
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.034 0.024 -10000 0 -0.21 2 2
SIRT1/Histone H1b 0.016 0.049 -10000 0 -0.22 11 11
apoptosis -0.039 0.021 0.21 2 -10000 0 2
SIRT1/PGC1A -0.02 0.095 0.19 2 -0.21 106 108
p53/SIRT1 0.025 0.019 -10000 0 -0.25 2 2
SIRT1/FOXO4 0.011 0.047 -10000 0 -0.2 14 14
FOXO1/FHL2/SIRT1 0.036 0.031 -10000 0 -0.19 8 8
HIST1H1E 0.014 0.021 0.21 2 -10000 0 2
SIRT1/p300 0.029 0.02 -10000 0 -0.25 2 2
muscle cell differentiation -0.022 0.037 0.22 9 -0.21 2 11
TP53 0.02 0.016 0.35 1 -10000 0 1
KU70/SIRT1/BAX 0.04 0.021 -10000 0 -0.21 2 2
CREBBP 0.022 0.005 -10000 0 -10000 0 0
MEF2D 0.019 0.009 -10000 0 -10000 0 0
HIV-1 Tat/SIRT1 0.026 0.022 0.21 1 -0.25 2 3
ACSS2 -0.013 0.015 -10000 0 -0.25 2 2
SIRT1/PCAF/MYOD 0.022 0.037 0.21 2 -0.22 9 11
Signaling events mediated by HDAC Class II

Figure S114.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S114.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
G beta1gamma2/HDAC5 0.05 0.035 0.21 1 -0.19 7 8
HDAC3 0.023 0.003 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 -0.012 0.003 -10000 0 -10000 0 0
GATA1/HDAC4 0.031 0.007 -10000 0 -10000 0 0
GATA1/HDAC5 0.029 0.009 -10000 0 -10000 0 0
GATA2/HDAC5 0.007 0.079 -10000 0 -0.24 47 47
HDAC5/BCL6/BCoR 0.039 0.02 -10000 0 -0.21 1 1
HDAC9 0.016 0.049 -10000 0 -0.35 9 9
Glucocorticoid receptor/Hsp90/HDAC6 0.005 0.09 -10000 0 -0.21 78 78
HDAC4/ANKRA2 0.031 0.015 -10000 0 -0.24 1 1
HDAC5/YWHAB 0.031 0.01 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.009 0.003 -10000 0 -10000 0 0
GATA2 -0.011 0.11 -10000 0 -0.35 47 47
HDAC4/RFXANK 0.033 0.017 0.22 3 -10000 0 3
BCOR 0.023 0.003 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
HDAC10 0.021 0.007 -10000 0 -10000 0 0
HDAC5 0.022 0.005 -10000 0 -10000 0 0
GNB1/GNG2 0.028 0.038 0.21 1 -0.24 9 10
Histones 0.004 0.059 -10000 0 -0.29 6 6
ADRBK1 0.022 0.004 -10000 0 -10000 0 0
HDAC4 0.023 0.004 -10000 0 -10000 0 0
XPO1 0.023 0.003 -10000 0 -10000 0 0
HDAC5/ANKRA2 0.031 0.016 -10000 0 -0.24 1 1
HDAC4/Ubc9 0.032 0.009 -10000 0 -10000 0 0
HDAC7 0.022 0.005 -10000 0 -10000 0 0
HDAC5/14-3-3 E 0.031 0.01 -10000 0 -10000 0 0
TUBA1B 0.023 0.002 -10000 0 -10000 0 0
HDAC6 0.023 0.004 -10000 0 -10000 0 0
HDAC5/RFXANK 0.032 0.015 0.21 2 -10000 0 2
CAMK4 0.022 0.038 0.28 5 -0.35 3 8
Tubulin/HDAC6 0.044 0.02 0.2 3 -0.21 1 4
SUMO1 0.023 0.003 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
YWHAB 0.022 0.005 -10000 0 -10000 0 0
GATA1 0.019 0.005 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
YWHAE 0.021 0.007 -10000 0 -10000 0 0
NR3C1 -0.033 0.13 -10000 0 -0.35 78 78
SUMO1/HDAC4 0.024 0.043 -10000 0 -0.19 11 11
SRF 0.022 0.004 -10000 0 -10000 0 0
HDAC4/YWHAB 0.032 0.009 -10000 0 -10000 0 0
Tubulin 0.033 0.023 0.21 3 -0.24 2 5
HDAC4/14-3-3 E 0.031 0.01 -10000 0 -10000 0 0
GNB1 0.022 0.004 -10000 0 -10000 0 0
RANGAP1 0.021 0.006 -10000 0 -10000 0 0
BCL6/BCoR 0.03 0.016 -10000 0 -0.24 1 1
HDAC4/HDAC3/SMRT (N-CoR2) 0.044 0.012 -10000 0 -10000 0 0
HDAC4/SRF 0.044 0.024 0.2 4 -0.21 2 6
HDAC4/ER alpha 0.003 0.085 -10000 0 -0.24 54 54
EntrezGene:23225 0 0 -10000 0 -10000 0 0
positive regulation of chromatin silencing 0.004 0.059 -10000 0 -0.29 6 6
cell motility 0.044 0.02 0.2 3 -0.21 1 4
EntrezGene:23636 0 0 -10000 0 -10000 0 0
UBE2I 0.022 0.005 -10000 0 -10000 0 0
HDAC7/HDAC3 0.032 0.009 -10000 0 -10000 0 0
BCL6 0.02 0.018 -10000 0 -0.35 1 1
HDAC4/CaMK II delta B 0.023 0.004 -10000 0 -10000 0 0
Hsp90/HDAC6 0.032 0.008 -10000 0 -10000 0 0
ESR1 -0.017 0.11 -10000 0 -0.35 54 54
HDAC6/HDAC11 0.032 0.009 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.026 0.041 -10000 0 -0.18 9 9
NPC 0.014 0.001 -10000 0 -10000 0 0
MEF2C -0.011 0.11 -10000 0 -0.35 46 46
RAN 0.023 0.003 -10000 0 -10000 0 0
HDAC4/MEF2C 0.041 0.07 -10000 0 -0.18 44 44
GNG2 0.017 0.05 0.28 1 -0.35 9 10
NCOR2 0.023 0.004 -10000 0 -10000 0 0
TUBB2A 0.022 0.031 0.28 3 -0.35 2 5
HDAC11 0.023 0.014 0.33 1 -10000 0 1
HSP90AA1 0.022 0.004 -10000 0 -10000 0 0
RANBP2 0.023 0.002 -10000 0 -10000 0 0
ANKRA2 0.021 0.017 -10000 0 -0.35 1 1
RFXANK 0.024 0.021 0.3 3 -10000 0 3
nuclear import -0.025 0.01 -10000 0 -10000 0 0
Arf6 trafficking events

Figure S115.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S115.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SLC2A4 -0.16 0.18 -10000 0 -0.35 246 246
CLTC 0.01 0.066 -10000 0 -0.47 8 8
calcium ion-dependent exocytosis 0.007 0.03 -10000 0 -0.3 3 3
Dynamin 2/GTP 0.019 0.007 -10000 0 -10000 0 0
EXOC4 0.022 0.005 -10000 0 -10000 0 0
CD59 0.005 0.047 -10000 0 -0.38 7 7
CPE -0.012 0.064 -10000 0 -0.2 51 51
CTNNB1 0.022 0.004 -10000 0 -10000 0 0
membrane fusion 0.009 0.015 -10000 0 -10000 0 0
CTNND1 -0.009 0.027 0.18 10 -10000 0 10
DNM2 0.021 0.007 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.008 0.046 0.18 2 -0.38 4 6
TSHR 0.008 0.03 0.14 18 -0.2 3 21
INS -0.01 0.11 -10000 0 -0.48 24 24
BIN1 0.02 0.033 -10000 0 -0.35 4 4
mol:Choline 0.009 0.015 -10000 0 -10000 0 0
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP 0.009 0.003 -10000 0 -10000 0 0
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0.023 0.003 -10000 0 -10000 0 0
mol:Ca2+ 0.018 0.007 -10000 0 -10000 0 0
JUP 0.006 0.042 -10000 0 -0.39 5 5
ASAP2/amphiphysin II 0.04 0.021 -10000 0 -0.19 3 3
ARF6/GTP 0.017 0.003 -10000 0 -10000 0 0
CDH1 0.005 0.042 -10000 0 -0.39 5 5
clathrin-independent pinocytosis 0.017 0.003 -10000 0 -10000 0 0
MAPK8IP3 0.022 0.005 -10000 0 -10000 0 0
positive regulation of endocytosis 0.017 0.003 -10000 0 -10000 0 0
EXOC2 0.022 0.005 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading 0.01 0.038 -10000 0 -0.3 3 3
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0.022 0.005 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.027 0.047 0.36 4 -10000 0 4
positive regulation of phagocytosis 0.009 0.002 -10000 0 -10000 0 0
ARF6/GTP/JIP3 0.029 0.008 -10000 0 -10000 0 0
ACAP1 0.01 0.031 -10000 0 -0.23 4 4
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 0.006 0.041 -10000 0 -0.35 6 6
clathrin heavy chain/ACAP1 0.01 0.056 -10000 0 -0.38 7 7
JIP4/KLC1 0.041 0.013 -10000 0 -10000 0 0
EXOC1 0.023 0.003 -10000 0 -10000 0 0
exocyst 0.01 0.039 -10000 0 -0.3 3 3
RALA/GTP 0.017 0.003 -10000 0 -10000 0 0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0.029 0.008 -10000 0 -10000 0 0
receptor recycling 0.017 0.003 -10000 0 -10000 0 0
CTNNA1 -0.01 0.024 0.18 8 -10000 0 8
NME1 0.009 0.003 -10000 0 -10000 0 0
clathrin coat assembly 0.01 0.07 0.26 1 -0.47 8 9
IL2RA 0.008 0.049 -10000 0 -0.36 7 7
VAMP3 0.01 0.002 -10000 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 -0.057 0.094 -10000 0 -0.38 9 9
EXOC6 0.022 0.005 -10000 0 -10000 0 0
PLD1 0.008 0.007 -10000 0 -10000 0 0
PLD2 0.009 0.005 -10000 0 -10000 0 0
EXOC5 0.022 0.004 -10000 0 -10000 0 0
PIP5K1C 0.006 0.038 -10000 0 -0.5 2 2
SDC1 0.019 0.045 0.2 1 -0.35 5 6
ARF6/GDP 0.019 0.005 -10000 0 -10000 0 0
EXOC7 0.022 0.006 -10000 0 -10000 0 0
E-cadherin/beta catenin 0.029 0.049 -10000 0 -0.37 4 4
mol:Phosphatidic acid 0.009 0.015 -10000 0 -10000 0 0
endocytosis -0.039 0.02 0.19 3 -10000 0 3
SCAMP2 0.022 0.005 -10000 0 -10000 0 0
ADRB2 -0.019 0.087 0.3 1 -0.44 9 10
EXOC3 0.022 0.006 -10000 0 -10000 0 0
ASAP2 0.022 0.005 -10000 0 -10000 0 0
Dynamin 2/GDP 0.021 0.008 -10000 0 -10000 0 0
KLC1 0.022 0.004 -10000 0 -10000 0 0
AVPR2 -0.038 0.1 0.23 7 -0.44 10 17
RALA 0.022 0.004 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.02 0.047 0.32 1 -0.35 4 5
p38 MAPK signaling pathway

Figure S116.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S116.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TRAF6/ASK1 0.014 0.021 -10000 0 -0.16 1 1
TRAF2/ASK1 0.028 0.014 -10000 0 -0.2 1 1
ATM 0.022 0.005 -10000 0 -10000 0 0
MAP2K3 -0.003 0.095 0.26 1 -0.34 25 26
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.006 0.089 0.28 3 -0.34 18 21
hyperosmotic response 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
GADD45G 0.013 0.056 -10000 0 -0.35 12 12
TXN 0.005 0.001 -10000 0 -10000 0 0
CALM1 0.022 0.004 -10000 0 -10000 0 0
GADD45A 0.023 0.002 -10000 0 -10000 0 0
GADD45B 0.021 0.006 -10000 0 -10000 0 0
MAP3K1 0.022 0.005 -10000 0 -10000 0 0
MAP3K6 0.022 0.004 -10000 0 -10000 0 0
MAP3K7 0.023 0.003 -10000 0 -10000 0 0
MAP3K4 0.022 0.004 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
ASK1/ASK2 0.032 0.014 -10000 0 -0.24 1 1
TAK1/TAB family 0.001 0.023 0.14 2 -0.16 3 5
RAC1/OSM/MEKK3 0.04 0.013 -10000 0 -10000 0 0
TRAF2 0.022 0.006 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.014 0.08 -10000 0 -0.31 17 17
TRAF6 0.005 0.001 -10000 0 -10000 0 0
RAC1 0.022 0.005 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
CAMK2B 0.064 0.098 0.28 85 -0.35 1 86
CCM2 0.023 0.004 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB 0.052 0.057 0.19 76 -0.2 1 77
MAPK11 0.019 0.024 -10000 0 -0.35 2 2
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 0.063 0.058 0.19 78 -0.19 2 80
OSM/MEKK3 0.032 0.009 -10000 0 -10000 0 0
TAOK1 0.009 0.012 -10000 0 -0.26 1 1
TAOK2 0.01 0.003 -10000 0 -10000 0 0
TAOK3 0.01 0.002 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0.022 0.004 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
MAP3K5 0.022 0.017 -10000 0 -0.35 1 1
MAP3K10 0.022 0.005 -10000 0 -10000 0 0
MAP3K3 0.022 0.005 -10000 0 -10000 0 0
TRX/ASK1 0.013 0.03 -10000 0 -0.19 1 1
GADD45/MTK1/MTK1 0.043 0.037 -10000 0 -0.18 11 11
Class I PI3K signaling events

Figure S117.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S117.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ARF5/GTP -0.021 0.028 -10000 0 -10000 0 0
DAPP1 0.022 0.081 0.25 14 -0.36 7 21
Src family/SYK family/BLNK-LAT/BTK-ITK 0.016 0.11 0.31 4 -0.46 12 16
mol:DAG 0.012 0.061 0.26 12 -0.18 2 14
HRAS 0.023 0.007 -10000 0 -10000 0 0
RAP1A 0.024 0.005 -10000 0 -10000 0 0
ARF5/GDP 0.011 0.072 0.19 3 -0.25 21 24
PLCG2 0.02 0.021 0.28 1 -0.35 1 2
PLCG1 0.022 0.005 -10000 0 -10000 0 0
ARF5 0.022 0.005 -10000 0 -10000 0 0
mol:GTP -0.017 0.026 0.14 12 -10000 0 12
ARF1/GTP -0.007 0.028 0.23 1 -10000 0 1
RHOA 0.022 0.005 -10000 0 -10000 0 0
YES1 0.022 0.005 -10000 0 -10000 0 0
RAP1A/GTP -0.017 0.028 0.15 12 -10000 0 12
ADAP1 -0.018 0.026 0.15 1 -10000 0 1
ARAP3 -0.017 0.026 0.14 12 -10000 0 12
INPPL1 0.023 0.003 -10000 0 -10000 0 0
PREX1 0.022 0.005 -10000 0 -10000 0 0
ARHGEF6 0.014 0.056 -10000 0 -0.35 12 12
ARHGEF7 0.022 0.005 -10000 0 -10000 0 0
ARF1 0.019 0.009 -10000 0 -10000 0 0
NRAS 0.024 0.005 -10000 0 -10000 0 0
FYN 0.022 0.004 -10000 0 -10000 0 0
ARF6 0.023 0.003 -10000 0 -10000 0 0
FGR 0.015 0.051 -10000 0 -0.35 10 10
mol:Ca2+ 0.009 0.052 0.19 28 -10000 0 28
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 0.013 0.058 -10000 0 -0.35 13 13
ZAP70 0.03 0.051 0.28 16 -0.35 2 18
mol:IP3 0.009 0.062 0.22 27 -0.15 1 28
LYN 0.021 0.007 -10000 0 -10000 0 0
ARF1/GDP 0.009 0.069 0.2 1 -0.28 10 11
RhoA/GDP 0.018 0.046 0.24 3 -0.22 1 4
PDK1/Src/Hsp90 0.042 0.015 -10000 0 -10000 0 0
BLNK 0.021 0.026 0.28 1 -0.35 2 3
actin cytoskeleton reorganization 0.003 0.067 0.26 12 -0.28 6 18
SRC 0.022 0.005 -10000 0 -10000 0 0
PLEKHA2 -0.012 0.01 -10000 0 -0.21 1 1
RAC1 0.022 0.005 -10000 0 -10000 0 0
PTEN 0.022 0.01 -10000 0 -10000 0 0
HSP90AA1 0.022 0.004 -10000 0 -10000 0 0
ARF6/GTP -0.02 0.03 -10000 0 -10000 0 0
RhoA/GTP -0.018 0.027 -10000 0 -10000 0 0
Src family/SYK family/BLNK-LAT 0.019 0.061 0.21 4 -0.29 7 11
BLK 0.037 0.067 0.28 36 -10000 0 36
PDPK1 0.022 0.005 -10000 0 -10000 0 0
CYTH1 -0.018 0.026 0.15 1 -10000 0 1
HCK 0.025 0.03 0.28 7 -10000 0 7
CYTH3 -0.019 0.026 0.15 1 -10000 0 1
CYTH2 -0.019 0.026 0.15 1 -10000 0 1
KRAS 0.023 0.014 0.31 1 -10000 0 1
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 0.006 0.035 -10000 0 -0.36 2 2
SGK1 0.012 0.037 -10000 0 -0.38 2 2
INPP5D 0.022 0.017 -10000 0 -0.35 1 1
mol:GDP -0.001 0.073 0.19 5 -0.25 22 27
SOS1 0.023 0.003 -10000 0 -10000 0 0
SYK 0.022 0.013 0.28 1 -10000 0 1
ARF6/GDP -0.012 0.043 0.21 5 -0.22 1 6
mol:PI-3-4-5-P3 -0.017 0.026 -10000 0 -10000 0 0
ARAP3/RAP1A/GTP -0.017 0.028 0.16 12 -10000 0 12
VAV1 0.023 0.031 0.28 5 -0.35 1 6
mol:PI-3-4-P2 -0.012 0.011 -10000 0 -0.24 1 1
RAS family/GTP/PI3K Class I 0.034 0.031 0.32 1 -0.15 1 2
PLEKHA1 -0.013 0.009 -10000 0 -0.21 1 1
Rac1/GDP 0.011 0.072 0.2 1 -0.25 19 20
LAT 0.022 0.005 -10000 0 -10000 0 0
Rac1/GTP 0 0.081 -10000 0 -0.29 30 30
ITK -0.023 0.034 -10000 0 -10000 0 0
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma 0.011 0.066 0.29 8 -0.25 2 10
LCK 0.024 0.028 0.28 4 -0.35 1 5
BTK -0.02 0.027 0.15 1 -10000 0 1
Signaling events mediated by HDAC Class I

Figure S118.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S118.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NF kappa B/RelA 0.057 0.072 0.23 2 -0.22 8 10
Ran/GTP/Exportin 1/HDAC1 -0.012 0.003 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.031 0.061 -10000 0 -0.28 8 8
SUMO1 0.023 0.003 -10000 0 -10000 0 0
ZFPM1 0.02 0.018 -10000 0 -0.35 1 1
NPC/RanGAP1/SUMO1/Ubc9 0.009 0.003 -10000 0 -10000 0 0
FKBP3 0.023 0.004 -10000 0 -10000 0 0
Histones 0.055 0.038 -10000 0 -10000 0 0
YY1/LSF 0.008 0.069 -10000 0 -0.23 30 30
SMG5 0.019 0.009 -10000 0 -10000 0 0
RAN 0.023 0.003 -10000 0 -10000 0 0
I kappa B alpha/HDAC3 0.026 0.029 0.17 6 -0.19 2 8
I kappa B alpha/HDAC1 0.032 0.034 -10000 0 -10000 0 0
SAP18 0.022 0.005 -10000 0 -10000 0 0
RELA 0.024 0.035 0.19 6 -0.17 2 8
HDAC1/Smad7 0.042 0.021 -10000 0 -0.21 2 2
RANGAP1 0.021 0.006 -10000 0 -10000 0 0
HDAC3/TR2 0.032 0.036 -10000 0 -10000 0 0
NuRD/MBD3 Complex 0.027 0.042 -10000 0 -0.35 1 1
NF kappa B1 p50/RelA 0.022 0.07 0.23 1 -0.3 12 13
EntrezGene:23225 0 0 -10000 0 -10000 0 0
GATA2 -0.011 0.11 -10000 0 -0.35 47 47
GATA1 0.019 0.005 -10000 0 -10000 0 0
Mad/Max 0.033 0.008 -10000 0 -10000 0 0
NuRD/MBD3 Complex/GATA1/Fog1 0.016 0.073 -10000 0 -0.35 7 7
RBBP7 0.023 0.003 -10000 0 -10000 0 0
NPC 0.014 0.001 -10000 0 -10000 0 0
RBBP4 0.02 0.028 -10000 0 -0.35 3 3
MAX 0.022 0.004 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
FBXW11 0.022 0.004 -10000 0 -10000 0 0
NFKBIA 0.021 0.022 -10000 0 -10000 0 0
KAT2B 0.017 0.046 -10000 0 -0.35 8 8
mol:GTP 0 0 -10000 0 -10000 0 0
SIN3/HDAC complex 0.011 0.028 -10000 0 -10000 0 0
SIN3 complex 0.052 0.02 -10000 0 -10000 0 0
SMURF1 0.022 0.004 -10000 0 -10000 0 0
CHD3 0.021 0.006 -10000 0 -10000 0 0
SAP30 0.022 0.004 -10000 0 -10000 0 0
EntrezGene:23636 0 0 -10000 0 -10000 0 0
NCOR1 0.021 0.007 -10000 0 -10000 0 0
YY1/HDAC3 0.014 0.058 -10000 0 -0.28 8 8
YY1/HDAC2 0.009 0.065 -10000 0 -0.22 27 27
YY1/HDAC1 0.012 0.061 -10000 0 -0.22 24 24
NuRD/MBD2 Complex (MeCP1) 0.027 0.044 -10000 0 -0.3 2 2
PPARG 0.011 0.069 0.19 5 -0.26 24 29
HDAC8/hEST1B 0.035 0.02 -10000 0 -10000 0 0
UBE2I 0.022 0.005 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.022 0.004 -10000 0 -10000 0 0
TNFRSF1A 0.022 0.004 -10000 0 -10000 0 0
HDAC3/SMRT (N-CoR2) 0.032 0.036 -10000 0 -10000 0 0
MBD3L2 0.016 0.005 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.041 0.021 -10000 0 -0.21 2 2
CREBBP 0.022 0.005 -10000 0 -10000 0 0
NuRD/MBD3/MBD3L2 Complex 0.02 0.069 -10000 0 -0.28 14 14
HDAC1 0.023 0.004 -10000 0 -10000 0 0
HDAC3 0.022 0.022 0.15 2 -0.14 2 4
HDAC2 0.023 0.003 -10000 0 -10000 0 0
YY1 0.009 0.025 -10000 0 -0.22 6 6
HDAC8 0.023 0.002 -10000 0 -10000 0 0
SMAD7 0.021 0.023 -10000 0 -0.35 2 2
NCOR2 0.023 0.004 -10000 0 -10000 0 0
MXD1 0.023 0.004 -10000 0 -10000 0 0
STAT3 0.014 0.005 -10000 0 -10000 0 0
NFKB1 0.022 0.017 -10000 0 -0.35 1 1
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.023 0.002 -10000 0 -10000 0 0
YY1/LSF/HDAC1 0.022 0.065 -10000 0 -0.21 26 26
YY1/SAP30/HDAC1 0.024 0.061 -10000 0 -0.2 24 24
EP300 0.021 0.006 -10000 0 -10000 0 0
STAT3 (dimer non-phopshorylated) 0.014 0.005 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.021 0.022 -10000 0 -10000 0 0
histone deacetylation 0.027 0.044 -10000 0 -0.3 2 2
STAT3 (dimer non-phopshorylated)/HDAC3 0.022 0.031 -10000 0 -0.24 1 1
nuclear export -0.035 0.02 -10000 0 -10000 0 0
PRKACA 0.022 0.005 -10000 0 -10000 0 0
GATAD2B 0.019 0.009 -10000 0 -10000 0 0
GATAD2A 0.022 0.005 -10000 0 -10000 0 0
GATA2/HDAC3 0.013 0.069 -10000 0 -0.19 38 38
GATA1/HDAC1 0.03 0.008 -10000 0 -10000 0 0
GATA1/HDAC3 0.029 0.037 -10000 0 -10000 0 0
CHD4 0.022 0.004 -10000 0 -10000 0 0
TNF-alpha/TNFR1A 0.052 0.061 0.21 61 -0.24 2 63
SIN3/HDAC complex/Mad/Max 0.016 0.048 -10000 0 -0.32 5 5
NuRD Complex 0.023 0.064 -10000 0 -0.32 8 8
positive regulation of chromatin silencing 0.052 0.036 -10000 0 -10000 0 0
SIN3B 0.022 0.005 -10000 0 -10000 0 0
MTA2 0.023 0.003 -10000 0 -10000 0 0
SIN3A 0.022 0.005 -10000 0 -10000 0 0
XPO1 0.023 0.003 -10000 0 -10000 0 0
SUMO1/HDAC1 0.026 0.041 -10000 0 -0.19 8 8
HDAC complex 0.054 0.024 -10000 0 -0.19 3 3
GATA1/Fog1 0.027 0.017 -10000 0 -0.25 1 1
FKBP25/HDAC1/HDAC2 0.044 0.012 -10000 0 -10000 0 0
TNF 0.053 0.089 0.28 64 -0.35 2 66
negative regulation of cell growth 0.016 0.048 -10000 0 -0.32 5 5
NuRD/MBD2/PRMT5 Complex 0.027 0.044 -10000 0 -0.3 2 2
Ran/GTP/Exportin 1 0.026 0.041 -10000 0 -0.18 9 9
NF kappa B/RelA/I kappa B alpha 0.02 0.055 0.18 5 -0.28 8 13
SIN3/HDAC complex/NCoR1 0.006 0.066 -10000 0 -0.3 14 14
TFCP2 0.019 0.036 -10000 0 -0.35 5 5
NR2C1 0.023 0.002 -10000 0 -10000 0 0
MBD3 0.021 0.006 -10000 0 -10000 0 0
MBD2 0.022 0.004 -10000 0 -10000 0 0
Arf6 downstream pathway

Figure S119.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S119.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLAUR 0.014 0.019 -10000 0 -10000 0 0
regulation of axonogenesis -0.003 0.023 0.24 4 -10000 0 4
myoblast fusion -0.02 0.027 -10000 0 -10000 0 0
mol:GTP 0.016 0.023 -10000 0 -0.16 8 8
regulation of calcium-dependent cell-cell adhesion -0.037 0.043 0.19 12 -10000 0 12
ARF1/GTP 0.024 0.023 -10000 0 -10000 0 0
mol:GM1 0.007 0.016 -10000 0 -10000 0 0
mol:Choline 0.003 0.014 -10000 0 -0.19 1 1
lamellipodium assembly 0.007 0.051 -10000 0 -0.36 8 8
MAPK3 0.016 0.016 -10000 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 0.037 0.043 -10000 0 -0.19 12 12
ARF1 0.019 0.009 -10000 0 -10000 0 0
ARF6/GDP 0.02 0.027 -10000 0 -10000 0 0
ARF1/GDP 0.018 0.039 -10000 0 -0.21 8 8
ARF6 0.029 0.009 -10000 0 -10000 0 0
RAB11A 0.022 0.005 -10000 0 -10000 0 0
TIAM1 0.012 0.059 -10000 0 -0.35 13 13
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.016 0.018 -10000 0 -10000 0 0
actin filament bundle formation -0.025 0.036 0.21 8 -10000 0 8
KALRN 0.009 0.023 -10000 0 -0.17 5 5
RAB11FIP3/RAB11A 0.032 0.009 -10000 0 -10000 0 0
RhoA/GDP 0.025 0.037 -10000 0 -0.21 8 8
NME1 0.022 0.008 -10000 0 -10000 0 0
Rac1/GDP 0.025 0.039 -10000 0 -0.22 8 8
substrate adhesion-dependent cell spreading 0.016 0.023 -10000 0 -0.16 8 8
cortical actin cytoskeleton organization 0.007 0.051 -10000 0 -0.36 8 8
RAC1 0.022 0.005 -10000 0 -10000 0 0
liver development 0.016 0.023 -10000 0 -0.16 8 8
ARF6/GTP 0.016 0.023 -10000 0 -0.16 8 8
RhoA/GTP 0.028 0.021 -10000 0 -0.12 6 6
mol:GDP 0.009 0.028 -10000 0 -0.22 6 6
ARF6/GTP/RAB11FIP3/RAB11A 0.041 0.02 -10000 0 -10000 0 0
RHOA 0.022 0.005 -10000 0 -10000 0 0
PLD1 0.012 0.017 -10000 0 -10000 0 0
RAB11FIP3 0.022 0.005 -10000 0 -10000 0 0
tube morphogenesis 0.007 0.051 -10000 0 -0.36 8 8
ruffle organization 0.003 0.023 -10000 0 -0.24 4 4
regulation of epithelial cell migration 0.016 0.023 -10000 0 -0.16 8 8
PLD2 0.013 0.017 -10000 0 -0.21 1 1
PIP5K1A 0.003 0.023 -10000 0 -0.24 4 4
mol:Phosphatidic acid 0.003 0.014 -10000 0 -0.19 1 1
Rac1/GTP 0.007 0.051 -10000 0 -0.36 8 8
TRAIL signaling pathway

Figure S120.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S120.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TNFSF10 0.02 0.037 0.33 3 -0.35 3 6
positive regulation of NF-kappaB transcription factor activity 0.022 0.045 0.24 3 -0.24 11 14
MAP2K4 0.006 0.041 0.24 1 -0.24 6 7
IKBKB 0.021 0.007 -10000 0 -10000 0 0
TNFRSF10B 0.02 0.008 -10000 0 -10000 0 0
TNFRSF10A 0.02 0.008 -10000 0 -10000 0 0
SMPD1 0.008 0.015 0.15 3 -0.15 2 5
IKBKG 0.023 0.003 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
TNFRSF10D 0.013 0.051 -10000 0 -0.35 10 10
TRAIL/TRAILR2 0.027 0.027 0.24 3 -0.24 2 5
TRAIL/TRAILR3 0.027 0.03 0.24 3 -0.24 3 6
TRAIL/TRAILR1 0.027 0.027 0.24 3 -0.24 2 5
TRAIL/TRAILR4 0.022 0.045 0.24 3 -0.24 11 14
TRAIL/TRAILR1/DAP3/GTP 0.028 0.028 0.22 2 -0.19 2 4
IKK complex 0.012 0.033 -10000 0 -10000 0 0
RIPK1 0.022 0.004 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
DAP3/GTP 0.014 0.007 -10000 0 -10000 0 0
MAPK3 -0.01 0.03 0.3 3 -0.24 3 6
MAP3K1 0.012 0.039 0.26 1 -0.21 6 7
TRAILR4 (trimer) 0.013 0.051 -10000 0 -0.35 10 10
TRADD 0.02 0.008 -10000 0 -10000 0 0
TRAILR1 (trimer) 0.02 0.008 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 0.014 0.026 0.17 1 -0.17 8 9
CFLAR 0.023 0.003 -10000 0 -10000 0 0
MAPK1 -0.01 0.026 0.3 2 -0.24 3 5
TRAIL/TRAILR1/FADD/TRADD/RIP 0.049 0.036 0.23 2 -0.18 2 4
mol:ceramide 0.008 0.015 0.15 3 -0.15 2 5
FADD 0.022 0.004 -10000 0 -10000 0 0
MAPK8 0.009 0.052 0.19 6 -0.24 6 12
TRAF2 0.022 0.006 -10000 0 -10000 0 0
TRAILR3 (trimer) 0.019 0.018 -10000 0 -0.35 1 1
CHUK 0.022 0.005 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD 0.036 0.028 0.23 2 -0.21 2 4
DAP3 0.018 0.009 -10000 0 -10000 0 0
CASP10 0.009 0.06 0.17 49 -0.36 2 51
JNK cascade 0.022 0.045 0.24 3 -0.24 11 14
TRAIL (trimer) 0.02 0.037 0.33 3 -0.35 3 6
TNFRSF10C 0.019 0.018 -10000 0 -0.35 1 1
TRAIL/TRAILR1/DAP3/GTP/FADD 0.034 0.031 0.22 1 -0.18 2 3
TRAIL/TRAILR2/FADD 0.036 0.028 0.23 2 -0.21 2 4
cell death 0.008 0.015 0.15 3 -0.15 2 5
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 0.014 0.026 0.17 1 -0.17 8 9
TRAILR2 (trimer) 0.02 0.008 -10000 0 -10000 0 0
CASP8 0.012 0.039 -10000 0 -0.54 2 2
negative regulation of caspase activity 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP 0.049 0.036 0.23 2 -0.18 2 4
Paxillin-dependent events mediated by a4b1

Figure S121.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S121.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CRKL 0.022 0.005 -10000 0 -10000 0 0
Rac1/GDP 0.02 0.012 -10000 0 -10000 0 0
DOCK1 0.018 0.04 -10000 0 -0.35 6 6
ITGA4 0.022 0.026 0.28 1 -0.35 2 3
RAC1 0.022 0.005 -10000 0 -10000 0 0
alpha4/beta7 Integrin 0.033 0.017 0.21 2 -0.24 1 3
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.021 0.006 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.042 0.022 0.2 1 -0.21 2 3
alpha4/beta7 Integrin/Paxillin 0.034 0.018 0.19 2 -0.19 1 3
lamellipodium assembly -0.006 0.093 -10000 0 -0.39 23 23
PIK3CA 0.02 0.018 -10000 0 -0.35 1 1
PI3K 0.026 0.03 -10000 0 -0.24 5 5
ARF6 0.023 0.003 -10000 0 -10000 0 0
TLN1 0.022 0.005 -10000 0 -10000 0 0
PXN -0.011 0.003 -10000 0 -10000 0 0
PIK3R1 0.018 0.037 -10000 0 -0.35 5 5
ARF6/GTP 0.041 0.023 -10000 0 -0.17 2 2
cell adhesion 0.041 0.023 -10000 0 -0.18 2 2
CRKL/CBL 0.031 0.01 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin 0.032 0.02 0.19 1 -0.19 2 3
ITGB1 0.022 0.004 -10000 0 -10000 0 0
ITGB7 0.023 0.012 0.28 1 -10000 0 1
ARF6/GDP 0.021 0.012 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 0.029 0.061 0.2 1 -0.19 33 34
p130Cas/Crk/Dock1 0.036 0.032 -10000 0 -0.21 6 6
VCAM1 -0.005 0.098 -10000 0 -0.35 39 39
alpha4/beta1 Integrin/Paxillin/Talin 0.043 0.023 -10000 0 -0.18 2 2
alpha4/beta1 Integrin/Paxillin/GIT1 0.043 0.023 -10000 0 -0.18 2 2
BCAR1 0.02 0.007 -10000 0 -10000 0 0
mol:GDP -0.041 0.023 0.18 2 -10000 0 2
CBL 0.022 0.005 -10000 0 -10000 0 0
PRKACA 0.022 0.005 -10000 0 -10000 0 0
GIT1 0.022 0.005 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton 0.043 0.023 -10000 0 -0.18 2 2
Rac1/GTP -0.008 0.1 -10000 0 -0.44 23 23
VEGFR1 specific signals

Figure S122.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S122.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR1 homodimer/VEGFB homodimer 0.024 0.008 -10000 0 -10000 0 0
VEGFR1 homodimer/NRP1 0.008 0.002 -10000 0 -10000 0 0
mol:DAG -0.011 0.016 0.18 3 -10000 0 3
VEGFR1 homodimer/NRP1/VEGFR 121 0.022 0.007 -10000 0 -10000 0 0
CaM/Ca2+ 0.02 0.013 -10000 0 -10000 0 0
HIF1A 0.026 0.005 -10000 0 -10000 0 0
GAB1 0.019 0.033 -10000 0 -0.35 4 4
AKT1 0.002 0.055 0.48 1 -10000 0 1
PLCG1 -0.011 0.016 0.19 3 -10000 0 3
NOS3 0.014 0.049 0.43 2 -0.35 1 3
CBL 0.022 0.005 -10000 0 -10000 0 0
mol:NO 0.02 0.065 0.36 8 -0.34 1 9
FLT1 0.011 0.003 -10000 0 -10000 0 0
PGF 0.023 0.012 0.28 1 -10000 0 1
VEGFR1 homodimer/NRP2/VEGFR121 0.025 0.048 -10000 0 -0.19 20 20
CALM1 0.022 0.004 -10000 0 -10000 0 0
PIK3CA 0.02 0.018 -10000 0 -0.35 1 1
eNOS/Hsp90 0.027 0.057 0.28 4 -0.32 1 5
endothelial cell proliferation -0.009 0.064 0.34 3 -0.28 4 7
mol:Ca2+ -0.011 0.016 0.18 3 -10000 0 3
MAPK3 -0.019 0.046 0.31 5 -10000 0 5
MAPK1 -0.02 0.047 0.34 4 -10000 0 4
PIK3R1 0.018 0.037 -10000 0 -0.35 5 5
PLGF homodimer 0.023 0.012 0.28 1 -10000 0 1
PRKACA 0.022 0.005 -10000 0 -10000 0 0
RP11-342D11.1 0 0 -10000 0 -10000 0 0
CAV1 -0.041 0.14 -10000 0 -0.35 88 88
VEGFA homodimer 0.023 0.003 -10000 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer 0.024 0.008 -10000 0 -10000 0 0
platelet activating factor biosynthetic process -0.021 0.045 0.33 4 -10000 0 4
PI3K 0.04 0.03 -10000 0 -10000 0 0
PRKCA -0.021 0.036 0.17 1 -10000 0 1
PRKCB -0.021 0.039 0.18 3 -10000 0 3
VEGFR1 homodimer/PLGF homodimer 0.024 0.011 0.2 1 -10000 0 1
VEGFA 0.023 0.003 -10000 0 -10000 0 0
VEGFB 0.022 0.004 -10000 0 -10000 0 0
mol:IP3 -0.011 0.016 0.18 3 -10000 0 3
RASA1 -0.012 0.026 0.18 5 -10000 0 5
NRP2 0.006 0.078 -10000 0 -0.35 24 24
VEGFR1 homodimer 0.011 0.003 -10000 0 -10000 0 0
VEGFB homodimer 0.022 0.004 -10000 0 -10000 0 0
NCK1 0.021 0.023 -10000 0 -0.35 2 2
eNOS/Caveolin-1 0.002 0.089 0.45 4 -0.29 4 8
PTPN11 0.023 0.003 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.039 0.03 -10000 0 -10000 0 0
mol:L-citrulline 0.02 0.065 0.36 8 -0.34 1 9
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP 0.046 0.017 -10000 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer/NCK1 0.034 0.019 -10000 0 -0.19 2 2
CD2AP 0.022 0.004 -10000 0 -10000 0 0
PI3K/GAB1 0.047 0.037 -10000 0 -10000 0 0
PDPK1 -0.002 0.054 0.33 1 -10000 0 1
VEGFR1 homodimer/VEGFA homodimer/SHP2 0.035 0.012 -10000 0 -10000 0 0
mol:NADP 0.02 0.065 0.36 8 -0.34 1 9
HSP90AA1 0.022 0.004 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.044 0.017 -10000 0 -10000 0 0
VEGFR1 homodimer/NRP2 0.014 0.048 -10000 0 -0.2 24 24
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

Figure S123.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S123.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SMAD4 0.022 0.005 -10000 0 -10000 0 0
SMAD2 0.002 0.042 0.22 6 -0.27 3 9
SMAD3 0.013 0.024 -10000 0 -0.25 1 1
SMAD3/SMAD4 0.018 0.095 -10000 0 -0.48 16 16
SMAD4/Ubc9/PIASy 0.041 0.016 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4 0.045 0.053 0.24 3 -0.28 1 4
PPM1A 0.022 0.004 -10000 0 -10000 0 0
CALM1 0.022 0.004 -10000 0 -10000 0 0
SMAD2/SMAD4 0.014 0.041 0.22 3 -0.24 4 7
MAP3K1 0.022 0.005 -10000 0 -10000 0 0
TRAP-1/SMAD4 0.028 0.035 -10000 0 -0.24 8 8
MAPK3 0.022 0.005 -10000 0 -10000 0 0
MAPK1 0.022 0.005 -10000 0 -10000 0 0
NUP214 0.021 0.006 -10000 0 -10000 0 0
CTDSP1 0.023 0.003 -10000 0 -10000 0 0
CTDSP2 0.023 0.001 -10000 0 -10000 0 0
CTDSPL 0.022 0.004 -10000 0 -10000 0 0
KPNB1 0.022 0.005 -10000 0 -10000 0 0
TGFBRAP1 0.017 0.046 -10000 0 -0.35 8 8
UBE2I 0.022 0.005 -10000 0 -10000 0 0
NUP153 0.022 0.017 -10000 0 -0.35 1 1
KPNA2 0.034 0.057 0.3 23 -10000 0 23
PIAS4 0.021 0.006 -10000 0 -10000 0 0
PLK2 and PLK4 events

Figure S124.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S124.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLK2 0.021 0.017 -10000 0 -0.35 1 1
PLK4 0.025 0.025 0.28 5 -10000 0 5
regulation of centriole replication -0.011 0.015 0.11 4 -0.24 1 5
Arf1 pathway

Figure S125.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S125.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
coatomer protein complex 0.007 0.031 0.15 21 -10000 0 21
EntrezGene:79658 0 0 -10000 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.028 0.056 0.14 76 -0.18 6 82
AP2 0.03 0.011 -10000 0 -10000 0 0
mol:DAG 0 0 -10000 0 -10000 0 0
Arfaptin 2/Rac/GTP 0.026 0.014 -10000 0 -10000 0 0
CLTB 0.023 0.004 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ER cargo protein 0.012 0.008 -10000 0 -10000 0 0
CD4 0.023 0.012 0.28 1 -10000 0 1
CLTA 0.022 0.005 -10000 0 -10000 0 0
mol:GTP -0.001 0.002 -10000 0 -10000 0 0
ARFGAP1 -0.006 0.001 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.003 0.01 -10000 0 -0.14 1 1
ARF1/GTP 0.021 0.016 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein 0.005 0.004 -10000 0 -10000 0 0
mol:Choline 0.003 0.01 -10000 0 -0.14 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
ARF1 0.021 0.01 -10000 0 -10000 0 0
DDEF1 0.002 0.011 -10000 0 -0.15 1 1
ARF1/GDP 0.001 0.018 -10000 0 -0.11 3 3
AP2M1 0.021 0.007 -10000 0 -10000 0 0
EntrezGene:1313 0 0 -10000 0 -10000 0 0
actin filament polymerization -0.004 0.011 -10000 0 -10000 0 0
Rac/GTP 0.019 0.008 -10000 0 -10000 0 0
ARF1/GTP/GGA3/ARF-GAP1 0.025 0.016 -10000 0 -10000 0 0
ARFIP2 0.01 0.019 -10000 0 -10000 0 0
COPA 0.019 0.009 -10000 0 -10000 0 0
RAC1 0.022 0.005 -10000 0 -10000 0 0
ARF1/GTP/coatomer protein complex 0.01 0.027 -10000 0 -0.24 1 1
ARF1/GTP/ARHGAP10 0.013 0.008 -10000 0 -10000 0 0
GGA3 0.022 0.006 -10000 0 -10000 0 0
ARF1/GTP/Membrin 0.008 0.047 -10000 0 -0.2 21 21
AP2A1 0.022 0.004 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 0.007 0.022 -10000 0 -0.18 6 6
ARF1/GDP/Membrin 0.009 0.056 -10000 0 -0.24 23 23
Arfaptin 2/Rac/GDP 0.021 0.018 -10000 0 -10000 0 0
CYTH2 0.027 0.01 -10000 0 -10000 0 0
ARF1/GTP/GGA3 0.025 0.014 -10000 0 -10000 0 0
mol:ATP 0 0 -10000 0 -10000 0 0
Rac/GDP 0.016 0.003 -10000 0 -10000 0 0
mol:Brefeldin A 0 0 -10000 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex/Coatomer protein complex/ARF1/GTP 0.011 0.019 -10000 0 -0.17 1 1
PLD2 0.003 0.01 -10000 0 -0.14 1 1
ARF-GAP1/v-SNARE -0.006 0.001 -10000 0 -10000 0 0
PIP5K1A 0.003 0.01 -10000 0 -0.14 1 1
ARF1/GTP/Membrin/GBF1/p115 0.011 0.021 -10000 0 -0.12 3 3
mol:Phosphatic acid 0 0 -10000 0 -10000 0 0
mol:Phosphatidic acid 0.003 0.01 -10000 0 -0.14 1 1
KDEL Receptor/Ligand/ARF-GAP1 -0.006 0.001 -10000 0 -10000 0 0
GOSR2 0.006 0.026 -10000 0 -0.32 3 3
USO1 0.005 0.029 -10000 0 -0.32 4 4
GBF1 0.005 0.032 -10000 0 -0.35 4 4
ARF1/GTP/Arfaptin 2 0.025 0.015 -10000 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex 0.041 0.018 0.2 1 -10000 0 1
a4b1 and a4b7 Integrin signaling

Figure S126.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S126.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ITGB1 0.022 0.004 -10000 0 -10000 0 0
ITGB7 0.023 0.012 0.28 1 -10000 0 1
ITGA4 0.022 0.026 0.28 1 -0.35 2 3
alpha4/beta7 Integrin 0.033 0.017 0.21 2 -0.24 1 3
alpha4/beta1 Integrin 0.032 0.02 0.21 1 -0.24 2 3
Sumoylation by RanBP2 regulates transcriptional repression

Figure S127.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S127.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.023 0.004 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 -0.013 0.009 -10000 0 -10000 0 0
MDM2/SUMO1 0.024 0.044 -10000 0 -0.19 11 11
HDAC4 0.023 0.004 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC1 -0.013 0.009 -10000 0 -10000 0 0
SUMO1 0.023 0.003 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1 0.007 0.014 -10000 0 -0.26 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
XPO1 0 0.02 -10000 0 -10000 0 0
EntrezGene:23636 0 0 -10000 0 -10000 0 0
RAN 0.023 0.003 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.023 0.002 -10000 0 -10000 0 0
SUMO1/HDAC4 0.024 0.043 -10000 0 -0.19 11 11
SUMO1/HDAC1 0.026 0.041 -10000 0 -0.19 8 8
RANGAP1 0.021 0.006 -10000 0 -10000 0 0
MDM2/SUMO1/SUMO1 0.054 0.018 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0.009 0.003 -10000 0 -10000 0 0
Ran/GTP 0.014 0.038 -10000 0 -0.18 10 10
EntrezGene:23225 0 0 -10000 0 -10000 0 0
MDM2 0.023 0.002 -10000 0 -10000 0 0
UBE2I 0.022 0.005 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.013 0.041 0.18 6 -0.18 9 15
NPC 0.014 0.001 -10000 0 -10000 0 0
PIAS2 0.022 0.005 -10000 0 -10000 0 0
PIAS1 0.022 0.005 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
Atypical NF-kappaB pathway

Figure S128.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S128.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL3/RelA 0.032 0.012 0.21 1 -10000 0 1
FBXW11 0.022 0.004 -10000 0 -10000 0 0
NF kappa B1 p50/c-Rel 0.02 0.013 -10000 0 -0.21 1 1
NF kappa B1 p50/RelA/I kappa B alpha 0.023 0.036 0.19 5 -0.24 1 6
NFKBIA 0.012 0.022 -10000 0 -10000 0 0
MAPK14 0.022 0.004 -10000 0 -10000 0 0
NF kappa B1 p105/p50 0.02 0.013 -10000 0 -0.21 1 1
ARRB2 0.01 0.003 -10000 0 -10000 0 0
REL 0.023 0.003 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
BCL3/NF kappa B1 p50 0.019 0.015 0.2 1 -0.21 1 2
response to UV 0 0 -10000 0 -10000 0 0
NF kappa B1 p105/RelA 0.019 0.013 -10000 0 -0.21 1 1
PIK3CA 0.02 0.018 -10000 0 -0.35 1 1
NF kappa B1 p50 dimer 0.014 0.016 0.24 1 -0.24 1 2
PIK3R1 0.018 0.037 -10000 0 -0.35 5 5
NFKB1 -0.011 0.011 -10000 0 -0.25 1 1
RELA 0.022 0.004 -10000 0 -10000 0 0
positive regulation of anti-apoptosis 0.017 0.032 -10000 0 -0.25 2 2
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.022 0.035 -10000 0 -10000 0 0
SRC 0.022 0.005 -10000 0 -10000 0 0
PI3K 0.026 0.03 -10000 0 -0.24 5 5
NF kappa B1 p50/RelA 0.017 0.032 -10000 0 -0.25 2 2
IKBKB 0.021 0.007 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.022 0.004 -10000 0 -10000 0 0
SYK 0.022 0.013 0.28 1 -10000 0 1
I kappa B alpha/PIK3R1 0.021 0.044 0.2 5 -0.2 5 10
cell death 0.021 0.034 -10000 0 -10000 0 0
NF kappa B1 p105/c-Rel 0.02 0.013 -10000 0 -0.21 1 1
LCK 0.024 0.028 0.28 4 -0.35 1 5
BCL3 0.023 0.012 0.28 1 -10000 0 1
E-cadherin signaling events

Figure S129.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S129.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
E-cadherin/beta catenin-gamma catenin 0.038 0.028 -9999 0 -0.3 2 2
E-cadherin/beta catenin 0.028 0.021 -9999 0 -0.24 2 2
CTNNB1 0.022 0.004 -9999 0 -10000 0 0
JUP 0.021 0.017 -9999 0 -0.35 1 1
CDH1 0.019 0.024 -9999 0 -0.35 2 2
Circadian rhythm pathway

Figure S130.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S130.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
chromatin modification 0.039 0.02 -10000 0 -10000 0 0
CLOCK 0.024 0.003 -10000 0 -10000 0 0
TIMELESS/CRY2 0.029 0.02 -10000 0 -10000 0 0
DEC1/BMAL1 0.028 0.015 -10000 0 -0.25 1 1
ATR 0.022 0.005 -10000 0 -10000 0 0
NR1D1 0.012 0.01 -10000 0 -10000 0 0
ARNTL 0.023 0.017 -10000 0 -0.35 1 1
TIMELESS 0.013 0.016 -10000 0 -10000 0 0
NPAS2 0.021 0.036 -10000 0 -0.35 5 5
CRY2 0.022 0.004 -10000 0 -10000 0 0
mol:CO -0.005 0.004 -10000 0 -0.073 1 1
CHEK1 0.022 0.005 -10000 0 -10000 0 0
mol:HEME 0.005 0.004 0.073 1 -10000 0 1
PER1 0.02 0.018 -10000 0 -0.35 1 1
BMAL/CLOCK/NPAS2 0.048 0.029 -10000 0 -0.2 5 5
BMAL1/CLOCK 0.013 0.051 -10000 0 -10000 0 0
S phase of mitotic cell cycle 0.039 0.02 -10000 0 -10000 0 0
TIMELESS/CHEK1/ATR 0.039 0.02 -10000 0 -10000 0 0
mol:NADPH 0.005 0.004 0.073 1 -10000 0 1
PER1/TIMELESS 0.026 0.02 -10000 0 -10000 0 0
PER1-2 / CRY1-2 0 0 -10000 0 -10000 0 0
DEC1 0.016 0.005 -10000 0 -10000 0 0
Alternative NF-kappaB pathway

Figure S131.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S131.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer 0.031 0.01 -9999 0 -10000 0 0
FBXW11 0.022 0.004 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.022 0.004 -9999 0 -10000 0 0
CHUK 0.022 0.005 -9999 0 -10000 0 0
NF kappa B2 p100/RelB 0.059 0.025 -9999 0 -10000 0 0
NFKB1 0.022 0.017 -9999 0 -0.35 1 1
MAP3K14 0.022 0.005 -9999 0 -10000 0 0
NF kappa B1 p50/RelB 0.031 0.015 -9999 0 -0.24 1 1
RELB 0.022 0.004 -9999 0 -10000 0 0
NFKB2 0.022 0.005 -9999 0 -10000 0 0
NF kappa B2 p52/RelB 0.029 0.009 -9999 0 -10000 0 0
regulation of B cell activation 0.028 0.009 -9999 0 -10000 0 0
Inferred Pathway Levels Matrix

Table 3.  Get Full Table First 10 out of 7202 rows and 4 out of 519 columns in the PARADIGM inferred pathway levels matrix.

pid_entity TCGA.SL.A6JA TCGA.SL.A6J9 TCGA.SJ.A6ZJ TCGA.SJ.A6ZI
109_MAP3K5 -0.14 0.019 0.019 0.019
47_PPARGC1A -0.35 0.023 0.023 -0.35
105_BMP4 0.023 -0.35 0.023 0.023
105_BMP6 0.023 0.023 0.023 0.023
105_BMP7 0.023 0 0.023 0.023
105_BMP2 0.023 -0.35 0.023 0.023
131_RELN/VLDLR -0.19 0 0.06 -0.19
30_TGFB1/TGF beta receptor Type II 0.023 0.023 0.02 0.023
84_STAT5B -0.031 0.029 -0.031 0.024
84_STAT5A -0.031 0.029 -0.031 0.024
Methods & Data
Input

  • Expression Data Normalization = Normal controls were used to median center the expression data used in this analysis.

  • mRNASeq Expression File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/mRNAseq_preprocessor/UCEC-TP/9831132/UCEC-TP.uncv2.mRNAseq_RSEM_normalized_log2_PARADIGM.txt

  • Copy Number File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Gistic2/UCEC-TP/10006362/GDAC_Gistic2Report_10008685/all_data_by_genes.txt

Data Sets and Pathway Interactions

Both copy number and expression data are incorporated into PARADIGM's inference. Whenever normal tissue controls are available for analysis in the expression data, each patient's gene-value is normalized by subtracting the gene's median level observed in the normal control. Copy number data is also normalized to reflect the difference in copy number between a gene's levels detected in tumor versus control (e.g. blood normal). The collection of pathways used by PARADIGM includes those from NCI-PID on September 15, 2009 containing 131 pathways, 11,563 interactions, and 7,204 entities. All gene identifiers were translated into HUGO standard identifiers wherever possible. We refer to molecular entities as "concepts," which include gene products such as proteins and miRNAs, small molecules, protein complexes, and abstract concepts. Each concept is represented as "node" in PARADIGM's graphical model. The abstract concepts correspond to general cellular processes (such as "apoptosis" or "DNA damage response") and families of genes that share functional activity such as the RAS family of signal transducers. Various types of concept-concept interactions are included in the pathways including protein-protein interactions, transcriptional regulatory interactions, and protein modifications such as phosphorylation and ubiquitinylation interactions.

Pathway Inference Method

The PARADIGM algorithm (described in PMID: 20529912) assigns an integrated pathway level (IPL) reflecting the activity of a concept determined through a belief propagation strategy. The belief propagation is given the copy number and gene expression measurements of all of the genes and iteratively updates hidden states reflecting the activities of all of the genes in a pathway so as to maximize the likelihood of the observed data given the interactions in the pathway. In the end, the inferred level of a concept reflects both the data observed for the concept and the neighborhood of activity surrounding the concept.

Determining significantly altered levels

The significance of the IPL obtained for each concept in each patient sample is assessed using a permutation analysis. Importantly, the permutation analysis preserves data tuples so as to preserve any implicit correlations between the different data modalities. For example, genes that are deleted have concomitantly lower expression levels. Preserving the copy number and expression pairs therefore retains this data property. The simulation therefore makes "null samples" by permuting data tuples across all of the genes in the genome so that each gene in a null sample is associated with a random tuple of another gene with equal probability. This approach has the added benefit of preserving the pathway structure so that every observed IPL can be compared to a distribution of random IPLs derived from exactly the same interaction context. PARADIGM inferences are then obtained for 1000 "null" patients and serve as a background distribution to contrast the observed IPLs against. Pathway concepts are excluded from further analysis if they did not obtain a minimum IPL of 0.5 in any patient sample both observed or simulated.

An IPL I(i,j) for concept i in sample j, is considered to be deviated if its absolute level is two standard deviations from the average level observed for concept i in the 1000 null samples. The degree to which a concept has significantly altered levels across a patient cohort is summarized in the proportion of deviated samples (PDS) score. For example, a protein with a PDS of 0.10 reflects that the protein's level of activity was inferred to be significantly higher or lower in tumors compared to normal in 10% of the patient samples. An average PDS for a pathway is also reported by computing the mean PDS over all concepts in the pathway.

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

References
[2] Charles J. Vaske, Stephen C. Benz, J. Zachary Sanborn, Dent Earl, Christopher Szeto, Jingchun Zhu, David Haussler, and Joshua M. Stuart, Inference of patient-specific pathway activities from multi-dimensional cancer genomics data using PARADIGM, Bioinformatics 12(26):237-245 (2010)
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